When I bought our Duramx Chevy and had the brake controller installed I "Assumed", (You got that right, "Assumed") that when the brake controller was hooked up that it would also charge the batteries. After a trip to Tom Johnson Camping Center, I learned that there is a fuse that has to go in one of the fuse boxes to make it charge while traveling too.
You may want to put your camper make and truck in your signature. (Look at the bottom of mine, it says I have the Flagstaff TT and the Duramax.)
Please let us know that you have found the problem.
2006 Flagstaff 831RLSS Travel Trailer
2007 Chevy 2500HD 'Classic' with the Duramax engine.
Converting a 1956 GMC PD4501 Scenicruiser, ex Greyhound into a motor home.