I had a battery temperature sensor code that caused the check engine light to stay on, im sure it was to do with that sensor at the bottom of the drivers side battery tray, so i simply jumped the terminals to make it go away until i buy a new sensor, which it did work. I had to remove the battery to get at the sensor, and after i finshed, went to start the truck up and noticed when you turn the key on, the voltage guage will go up to about 12.5volts (which is good) but then after one second it bottoms out to 0volts and the "check guages" light stays on at all times. I checked to see what my voltage is reading with a voltmeter from the batteries and it is reading fine, charging while running at 13 or 14 volts. So I removed my jumper wire for the batt temp sensorand it still has the problem.

What would cause the guage to do that? Is it a amperage draw or something. Bad brushes in alternator? Maybe since it has two batteries, something shorted out when i had the one battery out? I checked all the fuses seem ok. Thanks guys.

 

I'm not to sure did you try doing a load test on the batteries single them out. and load test them.
I can tell you that my Dodge 04.5 3500 CTD. When I first start it up the Alt isnt charging yet till its gets some RPM. then It starts charging.
As far what could be your problem I'm just not to sure what it could be