Hi,
I still don't think this is a computer problem. Unfortionately, without being there to see your wiring setup, it is hard to say what part of your wiring is causing the problem.
Somewhat Ironically, my Wrangler's alternator has decided it will no longer produce voltage above 13.5 volts -- which is NOT enough voltage to charge a 12 volt battery properly. So, right now I'm just putting a charger on the 12 volt battery for a few hours every other night to boost the battery back to a more fully charged state. Once I have time to fix the Alternator on my wrangler, I'll be more familiar with how the newer charging systems are wired, and then might have more ideas about your problems....
P.S. Did you ever get a voltage reading with the Jeep running and with it off? I'd really like to see these voltage readings.
-Nick :!: