Brake controller and power lock issues

OK I have a couple of weird problems that started at the same time so it makes me wonder if they're related. I did a tow with my 01 QC 4x4 1500 on Monday. Brake controller was working normally, as were the power door locks; I adjusted the brake controller after I loaded the vehicle I was hauling, and all was well. At the first gas stop we made, I noticed that I couldn't lock the doors with the power lock button on the door, although it would unlock the doors. I was able to use the key fob for the aftermarket alarm system to both lock and unlock the doors. A little later in the trip I noticed that the yellow pilot light on the brake control was not on, so I pulled over and reset the trailer plug (appears to be factory tow package). All trailer lights worked fine, but still no trailer brakes, so I just took it easy and made it home. I had a few minutes today to look at it, and now the power lock buttons (both doors) won't lock OR unlock the doors, although the key fob still works fine. Power lock fuse is good in the dash fuse box, and there are no blown fuses in the power box under the hood. Where the fuse for 'Trailer' is supposed to be under the hood is empty, as is the spot for a relay marked 'Trailer' so that made me wonder if it actually had a factory tow pack. There is an added on circuit breaker, along with an inline glass fuse, that are mounted on the power box that were obviously added on. This is a two conductor cable, with both wires (black and white) being wired hot from the battery lead on the power box. It looks like the cable goes into the cab, so I'm thinking this may be the brake control and 12volt wires for the trailer plug, but I ran out of time to follow up the wires today. Obviously, there is power to the power locks since they work with the aftermarket key fob; is there some type of body control module, or computer, that controls things like the door locks at the switches? I also had a brief episode of the transmission going into 'overdrive off' without me pushing the button, that only happened one time and did not reoccur. Any ideas would be great, I dont' have time to dig into it more until Friday but I need to get this fixed since I have more towing to do.