I recently installed the integrated trailer brake controller on my 2010 Ram 1500. I had the controller added to the BCM on Tuesday at the dealer. Took it home, hooked it up to the trailer and left it until Thursday morning. There was a message of service brake controller and the truck would not start until I unplugged the controller, any thoughts? I forgot to add that the controller worked until I had it added to the BCM
Getting back to Lee's original question, it sounds like your BCM got a bad flash. I would say to pull the connections from the brake controller and take the whole mess back to your dealer and get them to re-flash the BCM.
I don't know why people give the Mopar brake controller a bad name, I think a lot of people just don't know how to set one up! I have been towing trailers for as long as I have been driving and have used just about every style of brake controller made. NONE of them are perfect. I had a '98 RAM 2500 and have '12 RAM 2500, both with the OEM brake controller, both of them I purchased off of eBay and installed myself. The '98 just worked out of the box, the '12 I drove for over a year before having the dealer flash the BCM. They work fine, flashed or not.
Just stick a trailer on the ass end of the truck and get the horses running.