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TCM and PCM not communicating?

Hello fellow Dodge enthusiasts!! I have a 2006 Dodge Dakota R/T with the High Output V8 and automatic transmission (only 90,000 miles). I have a recurring problem - the Check Engine light occasionally comes on when I start it. I always carry my code scanner with me, and every time this happens, I'm getting codes for transmission issues (P0700, P0846, P0871, P0876, P0988, P0882). Sometimes, it will show 12 codes, but it's just the same six codes twice. Once in a while, it's only three or four of those codes. If I drive it this way, it's locked in third gear. I always read the codes then try to clear them; sometimes I can immediately. Sometimes, I get an ERROR message and it recommends I check my connection. I unplug the scanner, plug it back in and start over. When I finally DO get the codes cleared, the Check Engine light goes out and the truck runs/drives just fine. Local Dodge Dealer said they would do a quick 30 minute check of my truck for free (I know them well.) It was running fine when they checked it but they told me the TCM and PCM were not communicating at all. If that's the case, how does the truck run at all? And, how can I clear tranny codes if they're not communicating? Any fellow Dodge truck owners ever have a similar issue??? Thanks in advance for any and all suggestions.
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Anyway, I do appreciate your comments. I'm with you on "why is that power missing?" We just drove the truck to the grocery. I started the truck, pulled it into Drive and the check engine light came on. I pulled around to the side of the store, pulled out my hand-held scanner, and plugged it in. Just 4 of the codes were there. I shut the truck off, turned the key ON, then hit "Clear Codes" and got an ERROR on the screen. I unplugged the scanner, plugged it back in, and again read the codes. Same 4. I again hit "Clear Codes"; this time it recognized the command and asked for confirmation that I wanted the codes cleared. I hit YES, and it wiped them out. Turned the key OFF, then restarted the truck. She was fine all the way home. Very puzzling. The question becomes - Where am I losing power to the tranny? But yet, why is it restored so quickly/easily? Very odd..............
The service advisor at the dealer probably didn't say that the PCM and TCM weren't communicating at all unless he/she misinterpreted the information from the technician. The historical code for the loss of communication can only be retrieved after communication has been restored. All of the diagnostics have to be performed while the problem is actively occurring.
Some things that can happen that can cause a loss of communication include a loss of power or ground, and a circuit fault that is putting a load on the 5v reference output from the module. Have you tried to pull codes from all of the modules in the car? (ABS, Airbag, FCM/BCM, Instrument cluster, radio, HVAC as applicable ?)
The most important piece of information is how likely is this to occur in any one trip? Or once a day, once a week out of how many times does the truck get used, or????
Reading back just now, there is a common theme. All of the codes listed previously are for low voltage to those sensors/solenoids combine that with the loss of communication and the focus is already on specific circuits for the first step in the pinpoint testing. You reported that the codes set when starting. I'd be measuring system power (battery), switched input powers and grounds, communication circuits, and 5v reference with the DSO (digital storage oscilloscope) during start-up.
Right now the battery state of charge and cable connections cannot be ruled out.