The other problem that I have seen is very very rare. I emphasize rare. Its called shut down sequencing failure. This is what happens when the modules don't talk to the pcm when shutting down. When we shut our vehicles down, especially the ones mfgd in the last 10 years, a lot more happens than just turning off the key. The pcm likes to put all the modules "to bed" but if one of the modules isn't responding due to a intermitent connection the pcm cycles back through all the modules. It will keep doing this until its satisfied or the battery goes dead. All because one module isn't responding.
I have only seen this on 4 vehicles in the last 10 years and sometimes its a PIA to diagnose! Especially when the intermitent connection is present. Why am I emphasizing intermitent? Because a faulty module will throw a code. An intermitent module may be connected or disconnented, long enough in the sampling cycle for a code not to be important. Most of the time to diagnose the vehicle will have to be at the dealer overnight, maybe for one visit or possibly for multiple visits. I have seen this in 2 gms, 1 dodge, and 1 ford. Usually if this is the problem everthing on the charging/supply side has been replaced including cables and maybe even the battery twice.
I am pretty sure the OP's problem isn't this.
Lars
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