At this point I would highly suggest you start investigating ALL major electrical connections, cables, and grounds for tightness and corrosion. Check all major electrical connections on the truck for moisture and corrosion and when you take them apart reconnect with dielectric grease. Then check both batteries for condition by disconnecting them from each other and the truck and check their static voltage after sitting for a couple hours. They both should read exactly the same voltage, which would be around 12.5 - 12.6 if they're charged. Anything less and you'll want to replace them both with the same type, size, and brand.
Point is, it sounds like you're dealing with an electronic anomaly which can be common for these trucks because they're very sensitive to voltage/amperage levels and AC voltage feedback from alternator diodes/rectifier.