Inboard of the spare tire is the polarity protection device, or in your case it is called the LBCD. The battery power flows thru the manual disconnect, thru the remote disconnect(large relays) and to the LBCD. At the LBCD input it splits to the alternator. The LBCD has 2 large diode banks in it which prevent batteries connected incorrectly from killing the controllers and other electricals. The relays are controlled by those remote switches (under cab and under drivers dash) and by the LBCD if it detects alternator overload(keeps a bad oversized battery bank from killing the alternator).
what I suspect you are experiencing is a bad connection or relay contactor, probably on the 24v leg, somewhere along it’s path since you get 12v lights.
Voltage is only valid when tested under load... you can get full voltage fed thru a high resistance circuit throughout the circuit when unloaded But try and pull current thru that high resistance and the voltage will fall on it’s nose...
The first problem I experienced on my truck besides the ones it came with, was a fail to start shortly after I got my truck home. Would push the button and get a series of clicks. Had 12 and 24 at the PDP test points until I pushed the start button, then the 12V went to near zero and pulsed as the relays clicked. This turned out to be a badly corroded connection at the polarity box. Once I cleaned that up, voltage while cranking hardly differed from that measured at the batteries.
I suspect you have a similar issue and you need to measured loaded voltage along the circuit path from the batteries to PDP, to see where it is falling off. I mentioned the LBCD as located where it is between tire and air cleaner, it is out in the weather and subject to increased corrosion potential...
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