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Lincoln Navigator Electrical Problems

johnv8rjohnv8r Member Posts: 2
edited February 2015 in Lincoln
I have a '99 Lincoln Navigator. I'm in Northern CA. When it rains, my Navigator begins to have some strange electrical problems that last for anywhere from 2 to 7 days.

The symptoms are as follows:

1. When I shut the engine off, the ignition doesn't seem to want to completely shut off. The engine will shut down, but the ignition appears to still have some power. For example, I'll shut the door after getting out and the radio will turn back on or the lights on the dash will come on and begin flickering.

2. When I'm driving, I'll hear clicking sounds like a relay is going off. Today, the "Low Wiper Fluid" light would come on and go off several times a minute and the stereo would shut down...and yes, there is plenty of wiper fluid.

3. The battery will be dead after several hours of this electrical activity. I have to disconnect the battery to prevent it from draining overnight until water the problem is dries itself out. Then everything is back to normal with no lasting side effects.

The bottom line is there seems to be some type of water intrusion that is causing the ignition to remain on somehow.

Does anyone have any experience with this problem?




  • nvbankernvbanker Member Posts: 7,239
    I would have bet on your ignition switch being the culprit, but the water throws me a curve. I'd look for any leaks under the hood, or at the windshield seal at the firewall.... something is getting wet in there...
  • tonykeastonykeas Member Posts: 3
    I am very familar with your problem. I live in Chicago & have a 2000 Navigator, 3 years ago I went out to my Nav & the battery was dead?? Called the dealer because it was only about 2 weeks after I bought the truck & they replaced the batter without any questions asked. Now again about a month later it happened, so now my investigating skills went into action..... I got in the car & the radio was working & the dummy lights on the dash were blinking on & off spuratically... I got a hold of my friend whos a certified mechanic at the local Ford dealer (different than where I purchased the truck). I described him the exact problems you described & he said its the Gemm Module & another electrical brain box... I paid to have them both replaced & the problem was solved for a couple of months..... now the problem stated again... now I figured out that after it rains is when the truck acts up, they did a pressure test in the washer & found out that there was a leak comming from the sunroof, so I replaced the entire sunroof with a brand new one.... now 6 months later it happens again... IM FURIOUS... they now took apart the entire front part of the car, dash-console-headliner & all.... there was a leak comming from a crack in the firewall, we sent it to the body shop to have it re-welded & i have not had a problem for about a year now........ Good Luck, your going to have to tell them what to look for, because when they call their 800 tech line the tech line is going to tell them exactly to follow the same steps they followed with my problem.
  • cozy007cozy007 Member Posts: 2
    My heated seats on both sides stopped heating . i push the button on the seats and nothing happens there a fuse? This happened before on the passenger sideand the dealer fixed it in no time. i have looked for a fuse but didn't find one.
  • ljsgatorljsgator Member Posts: 5
    I have had my '04 ultimate for 2 months. I'm on my 3rd session with the dealer, and my second new battery. I read previous posts and I will say that 1 time it wouldn't start
    was after a car wash, and another was after a heavy rain.
    When I first got it I hauled a bunch of kids, and one claimed water came out of the rear dvd player. I have yet to see that. I contacted the former owner, and they claimed they were trouble free for 58k miles. I see no signs of water leaks inside the Gator. Where exactly should I look for water intrusion into the electrical system. What is a method of testing for a short.
  • rshakrshak Member Posts: 3
    ok here is my situation...I have a 2001 lincoln navigator w/some 24 inch as i was pulling out in reverse (wheels turned mind you) my truck just shut that. well it was still in gear so i tried to crank it up no luck, put in park tried to crank it up no luck the gears were locked...everything works but the truck wont crank. it is like it starts to crank but will not catch to crank up...PLEASE HELP!! lady in distress.... my freaking truck is at the dealership now and they are draining my pockets b/c they cant figure out what is wrong with my truck. they tried a new key but that did not work either.
  • gemini4evergemini4ever Member Posts: 1
    I have a 2001 Lincoln Nav. My moon roof is stuck in the open position. Any ideas on how to close manually if possible. Any help is appreicated
  • jwill242004jwill242004 Member Posts: 1
    Every now and then I am hearing what sounds like a police siren, in a short 2 second tone. It is coming from the rear of the vehicle inside the cab somewhere and I have no clue what it could be. Anyone heard of this?

  • unit576unit576 Member Posts: 3
    problems started with mysterious bell sound dinging in my dash. problems followed....lights on running boards stopped coming on, vehicle would not shift out of park, radio started turning on and off non stop, cruise control will not engage, interior lights stopped working, power windows stopped working(all 4), and wipers wont work either. it sounds like theres a relay or a soelinoid clicking under the dash. problems occured over a 2 day period and i'm stumped. someone please help!!!!!
  • ljsgatorljsgator Member Posts: 5
    I had a similar problem with my '04 right after I bought it. The dealership replaced the battery and all that stuff stopped. The new battery went dead, and they put in another one which also went dead. The dead battery issue was finally traced to the rear DVD player. I suspected they jump started the gator and zapped the player. They took it out and all went well. 3 weeks later I put it back in just to see what would happen.
    No problem. I think something in the player had to reboot. Every once in a while it does get confused and sticks out those running boards for no particular reason, or messes up the seat position. I just restart the gator and it straightens out. Nice Ride.
  • unit576unit576 Member Posts: 3
    tried replacing the battery and no luck. still same problems , all of them !!!! i was told to replace the fuse box and the GEM module. supposedly around these years theyve had problems with leaky windshields resulting in electrical problems. someone let me know if theyve heard of such things and /or have a solution for me....
  • ljsgatorljsgator Member Posts: 5
    I have no experience with a GEMM module. I guess you can start pulling fuses one at a time until you find the culprit. My dealership checked for water leaks and found it all dry. I went through 3 different trips to the dealership and 3 batteries and it turned out to be one circuit causing the battery drain.
  • imaloneimalone Member Posts: 1
    Hi all i have a 03 Lincoln Navigator in the uk and the climate contol ha sstoped working checked the fuses and relay but have no lights to the control unit in the center console any ideas please what to try next the rear fan does not work aswell but iam sure its goes through the contol panel please help a uk owner of a great American car. thanks Ian
  • wilfrwilfr Member Posts: 4
    Our 03 gator is giving us a lot of e-problems. Running boards, Liftgate, Battery,Dash lights,Air ride, Horn and now, coming back from xmas shopping at night and in the rain, the Tail lights and 4-way flasher failed!!!!!!! I'm sick and tired of this overpriced piece of junk. I'm more than disappointed in the Lincoln Navi !!!!
    Can somebody clue me in on some of my problems,please cheers,Wilfr
  • ljsgatorljsgator Member Posts: 5
    My '04 had similar issues that came up whenever water was around. My battery was replaced twice by the dealership, but the problem kept up until the DVD player was removed. It's like the player needed to be rebooted because I put it back in after 3 weeks and it works fine now. I would suggest you take it to the dealer and see if it needs a new battery.
    My problems started right after I bought it a year ago. I've been trouble free since then.
    No junk...nice ride.
  • wilfrwilfr Member Posts: 4
    Thanks for your info. "Junk" was in anger and disappointment. agree it is a nice ride, no doubt. Battery has just been replaced, no change!!!!! Now got the electrical schematics for everything and hope to shed some light on the problems. Our dealer wanted to change the motors for the liftgate and the runningboards, can't believe the price for these puppies, $ 750.00 for the runningboards before labour !!!!
    Anybody got some solid advise ???? Cheers,wilfr
  • ljsgatorljsgator Member Posts: 5
    Try pulling fuses one at a time. You may find the area that is the culprit. Something may need to be rebooted. I'd start with that rear DVD.
  • unit576unit576 Member Posts: 3
    hey buddy i found my problem in the fuse box. check all fuses that have to do with the GEM module. i believe mine was a 5 amp fuse but i cant remember. dont let those dealerships stroke you more than they may have all ready. i believe my problem stemmed from a leaky windshield seal that got the fuse box wet. good luck!!
  • jaycoxjaycox Member Posts: 4
    anyone out there can help me i have a 2000 navigator, the battery went dead last night, replaced it and it started just fine also the odometer light is on with the key off, just weird stuff happens now it wot start, lights come on automatically any help would be appreciated, thanks ron
  • buffy2buffy2 Member Posts: 1
    I am about to change the alternator on my 2000 Navigator.

    Is there a sequence that must be followed in this process?

    Also there is a switch clicking (machine gun like) when I now open the door will this disappear once I change the alternator? Is there a reset sequence. The battery is currently drained, but should be fine once I change the alternator as it was replaced 2 months ago.

    Any advice, Thanks

  • fhartfordfhartford Member Posts: 1
    I had a whistle like noise in the 3rd row area while driving and it turned out to be:
    A/C check value.
    replaced TXV per TSB (I am coping the tech. notes)
    part # FMC 6LIZ 19849 B
    valve asy- evaporat

    good luck
  • phylly06phylly06 Member Posts: 2
    Could someone please help me!!!!! I have my 2003 gator about 3 years now and as i was going to get it serviced..... my advancetrac light, ABS, brake lights and charging system started blinking and bells were sounding.... Make it to the dealership as all this was going on and the dealership stated that i needed a battery... purchased battery and that night ... same problem as before.
  • phylly06phylly06 Member Posts: 2
    After my 2003 gator charging system, ABS, brake light and advancetrac light was blinking and bells were ringing... The dealership stated that it was a battery problem.... Well that same day the battery was replaced , the problem continued... Come to find out that it was the alternator.. but this did now show up at the dealership. Dealership did not find the problem, my personal mechanic found the problem.. Navi is now a nice ride.
  • cfbtxcfbtx Member Posts: 3
    My drivers seat doesn't move on my 03 navi and I checked the fusees and replaced the one that was bad but it keeps burning the same fuse after I adjust my seat.
    Also every time I unlock my navi with the remote my mirrors go down as if I was going to reverse.
    Has anybody had any similar problems with there navigator?
  • joirhonejoirhone Member Posts: 3
    I have a 2004 Navigator that now when I go over a bump, the navigation panel flickers and turns a soft pink color. I can bang the top of the dash or the navigation panel itself and it works fine for awhile. What can be loose? Is it simple to pull apart the dash to check?
  • vcjvcj Member Posts: 1
    Hi, here's my issue. Left an interior light on and the battery died. Had to jump the car off, then replaced the battery. After jumping the car off the stereo system will not come on. Have checked all fuses and replaced #4, #7 and #22, just in case. Still no radio. Anybody have any suggestions? Thanks
  • speech1121speech1121 Member Posts: 1
    Our battery died and we replaced it--then the car started, but almost all the electrical features in the car would not work--no dashboard, radio, navigatiion, windows, hatch, seats. The only things we found that worked were the headlights, windshield wipers and air conditioning. Since we had the car we had random problems with the driver seat not working and the running boards not going in and out properly. The dealer says there was a leak in the car (?) and all the wiring harnesses are wet and corroded. The car never had a visible leak, and there is no musty smell or damp mats. Dealer said it will be $12,000 to $15,000 to fix and the car only has 38,000 miles and we are out of warantee. At first they sounded like they would help us with Lincoln to get it fixed, but now they say it is not due to the design of the car and Lincoln has no responsibility. My insurance said the car was never in a flood, so it is not eligibe for a comprehensive claim--so I am out one car, that cost $60,000 five years ago. Any suggestions?
  • akirbyakirby Member Posts: 8,062
    Find another dealer. Doesn't sound right to me. If there was a leak it had to come from somewhere - what did the dealer say?
  • bigc99703bigc99703 Member Posts: 1
    hi i have a 01 lincoln navigator and my service engine light will not turn off i just had the transmission rebuilt. i hooked up the machine to it and it gave me a code that said p0171 and p0174 could you tell me me what these codes mean.
  • akirbyakirby Member Posts: 8,062
    Do a google search for OBDII codes.
  • jeyhoejeyhoe Member Posts: 490
    Li'l Queenie here :P I did search for OBD II codes. Thanks for that kick, akirby. I didnt realize they were industry standard and that, eg P0171 and P0174 mean the same things on all vehicles and that is both the left bank (71) and the right bank (74) are running too lean. The P means Powertrain and the 0 means standard codes - if the first digit were a 1 instead, then the rest of the code would by manufacturer specific, eg if a Ford then P1169 could mean Honeywell turbo implosion imminent. ;) something like that.

    In any case, thanks I learned somethin today. Now I wish I could figure out why BOTH of my 1995 Ford econolines have intermittent CELs and never a code?
  • mark170mark170 Member Posts: 1
    For the last 3 weeks, my 98 Navigator will sometimes not start. The starter will turn but the motor won't fire. I brought it to both the dealer and a good mechanic, and of course, it started for them. They found no problems with it. I went out this morning after trying to start it again after work yesterday and now the back end is squatting down. It seems like the car is just about to roll over and play dead. I've checked all the fuses and battery and all is good. Any suggestions?

    Thanks, Mark
  • lilbit3lilbit3 Member Posts: 1
    I have a 2004 Navigator and since New Years Day I have had to be towed to the dealership 4 times and they can't seem to find the problem. Something in the electrical is completely draining the battery if it sits for 24 hours or more. They have replaced the battery and several sensors, cleaned conections on the running boards, door mirrors. They have hooked up to the computer which says nothing wrong. When I get a boost as soon as they hook up the cables it starts usually if its drained it should take a few minutes of being hooked up before there is power but not with mine there is power instantly which tells me its not draining the battery but its gotta be something electrical. Does anyone have any ideas cause Ford Lincoln can't figure it out. :confuse:
  • grimm1grimm1 Member Posts: 1
    I am unable to find the fuse for the dash lights on this vehicle. I can locate the fuse box, just don't have the location of the fuse for the dashboard lights. Any help would be appreciated. never got a manual with the used vehicle.

  • Navi_oneNavi_one Member Posts: 1
    I was having the same problem with my 04 Navigator. I came back from a trip and had to get a boost from the airport parking lot. Took it to the dealer and they said it was the alternator, but it wasn't. Changed the battery, but it still drained the day after. I had to take it to a shop to get diagnostics and a load test and it was a ground wire from the negative terminal of the battery that was causing all the problems. Does your panel lights come on on their own? This was the first thing i noticed when I came out my house to check on the car. All of the lights in the car and the side mirrors were on but the alarm was still on.
  • vjw757vjw757 Member Posts: 1

  • cfbtxcfbtx Member Posts: 3
    #1-I was warming up my Navigator Friday morning to go to work and my rear sensors went off but the truck was still in park. So I got off to see if anything was behind me but nothing. #2- Sometimes when I open the rear side windows only one opens, so I close it and push it again and then they both open.#3- The rear passenger door only locks/unlocks sometimes.
    In the 3 years I've had it I think it was way over priced and not worth it because they have too many problems but from the looks of things I guess I'm not the only one that has to put up with these headaches. :confuse:
    Good Luck
  • donavan71donavan71 Member Posts: 6
    I own a 2001 Navigator with factory Alpine radio system and having recently returned from Iraq, i noticed that i had no bass from the woofer.
    How do i go about troubleshooting this?

    thanx in advance!
  • mmaximommaximo Member Posts: 1
    the last few days the light that indicated that the 4x4 is on start to flash the the off light on the overdrive switch starts to flash too.what may be causig this?
    please HELP!!!!
  • BOSHOUSBOSHOUS Member Posts: 1
    ok i got this car in OCT of 2008 and everything was fine until the starter went out and once that was fixed the car was running smooth with no problems.....but the last two weeks have been horrible the car wont start after being at the dealership ( bout to go MOnday for the third time in one week) they get it to start then as soon as i get home the car wont start......HELP ME I REALLY NEED ADVICE im spending so much money on this what could be the problem?
  • jwallyjwally Member Posts: 71
    "tired of this overpriced piece of junk"
    My 01 has the same problem from water getting in dash from possible windshield,roof weatherstripping or roof rack, water flows in drivers pillar handle. damaged my GEM modular costing hundreds last year and having same problem now again. SOME ONE SHOULD GET A CLASSACTION SUIT AGAINST FORD WITH SO MANY ON HERE WITH SAME PROBLEM.
    i don't exactly know where waters coming in but have seen drips on handle and under dash.
  • jwallyjwally Member Posts: 71
    "Lincoln to get it fixed, but now they say it is not due to the design of the car and Lincoln has no responsibility. "

    How can so many people on here have the same problems and not be their responsibility? I have an 2001 with 70,000 miles and nothing but probelms
  • vizaldyvizaldy Member Posts: 3
    i have a 2000 nav with the same problems you have and mine is leaking water fronm top can't find where from but is going directly to the braim box behind the sterring wheel i'm mad and don;t know what to do
  • dneilsondneilson Member Posts: 1
    I just started having the identical issue with my '03 truck. Blew fuse #3 which controls power seats, mirrors, and memory seat settings. Changed the fuse many times. I then took the mirror switch out and changed the fuse. This provided me power to me electric seats and my memory presets were restored. I thought I needed to replace the mirror switch, but after $100.00 that was not the problem. Please let me know if you solved your problem, and what you did o get it fixed.
  • cfbtxcfbtx Member Posts: 3
    My navigator still has the same problems. I took it to the dealer and the excuse they came up with was that the computer might have gotten wet, which is a bunch of BS..... So they said they would recommend me to get a new computer. So I just gave up and tried to trade it in for a Escalade but the Cadillac dealer wouldn't take my navigator so I'm stuck with it.:(
  • bronconvictbronconvict Member Posts: 12
    2003 was obviously the worst year of all since it was the year they updated the older style. Searching a bit, you'll find this model year was notorious for the windshield leak defect which caused numerous electrical headaches. Particularly since the GEM module was at the core of many random electrical mishaps. This module is "i believe" located behind the fuse panel. A few corroded inners and sudenly your elctrical system parties in the middle of the night while the truck is off.

    There are many defects in the TSB's and being such an expensive purchase only adds to the headache.
  • jrutkowskijrutkowski Member Posts: 1
    MY 2006 navigator a/c quit 2 weeks ago. I checked all fuses listed in manual and all are good. Is there something I may have missed, like a relay box under the hood or something....
    Besides that, best SUV i've ever owned.......
  • jv_ictjv_ict Member Posts: 2
    HELP!!!!!!! We have a 2005 Lincoln Navigator and have run up against an issue that the dealership is even having trouble with. Our Navigator will begin unlocking itself repeatedly and will not stop for long durations of time. (20 + minutes). This is happening frequently enough it has now broke one of our door locks. The dealership replaced a security module about 1.5 months ago the problem ceased until recently. It is sporatic and we haven't been able to pin down what is causing it or get it to keep doing it long enough for the dealership to determine what is causing it. The dealership has ran through everything and they can't figure it out. They are supposed to send Lincoln technical suppport down to look at it but none of the dealerships in this area have ran up against this. We tried using the remote to lock and unlock it, opening and closing doors, and starting and stopping the engine. It will start unlocking itself day or night to the point it has ran our battery down several times. The crux of this problem is it has happened every where except for repeating itself long enough at the dealership so they can figure it out. HAS any one came accross this?
  • livemoorelivemoore Member Posts: 1
    Ugh! We're having the same problem. It's already run down our battery once. Did you ever get it fixed?

  • jv_ictjv_ict Member Posts: 2
    Yes we got it fixed,

    after the dealer ship replaced the security module, we were fine for over two months...then the problem fired up again. It would happen, then not happen, it would happend for 45 minutes, then not happen, then for 5 minutes, and so on with no pattern whatso ever. We figured out that after leaving it with dealership a few days (and the navigator was in the shop right next to someone the whole time) finally acted up in front of them. They figured out we had a defective remote...that was unlocking the hell out of it. It even broke one of our back lock cylinders. My suggestion to you if this sounds like something you are experiencing, would be throw all your remotes away and start fresh. They are about $50 a pop and its not terribly hard to reprogram the navigator. This frustrated the hell out of us because we couldn't figure out and neither did the dealership until they hung out with car for a few days. If you need more feedback, please post another message.
  • ratedr1ratedr1 Member Posts: 2
    I purchased a 2001 Navigator in 2003 and have had nothing but problems, 1 thing after another , worst vehicle i have ever owned, as well as the most expensive, most of the parts are made out of cheap plastic and 2x the price. The rubber on the parts is the lowest quality they could possibly use. In the Last 2 months I have had to spend $550 to fix a problem with the air ride suspension , $280 fuel sensor, $720 fuel pump, and today the stereo completely died and all the fuses are still good, DO NOT BUY A NAVIGATOR!!!! i am going to put signs on my vehicle and every saturday park it outside a different Lincoln dealership warning potential buyers to stay clear and save there money and sanity , anyone interested in starting a P/O Navigator Owners group email me at [email protected] . I spent 4.5 yrs making $600 a month payments to find out i would get less then $5000 on a trade...IF YOU ARE THINKING ABOUT BUYING A NAVIGATOR YOU WOULD BE BETTER OFF SPENDING YOUR MONEY ON CRACK!!!! It has caused me nothing but stress in my life, save yourself the agony and buy GM
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