Hi transistor,
Before you make any changes to your truck's mods, you have an ECU that does control your Security system, Keyless entry system, Power windows, Power doorlocks...etc! Every so often, the master ECU (Main body ECU compu network) will behave much like a Windows laptop when running out of free storage/RAM and will malfunction as a result!
So it too needs an occasional RE-BOOT AKA a master RESET! This restores the ECU's 'factory settings'; which sometimes are changed/corrupted because of all of the Temporary Files it stores e.g., history logs, error codes, travel data (MPG and learned operator behaviors), to name a few!
Since the Main body ECU controls about 26 or 27 other ecu's, I can't tell you which fuse to pull, but you can just disconnect the NEG battery cable and leave it disconnected for a very minimum time period of four hours...over-night would be better to be sure that ALL of the ecu modules are cleared of all corrupt software/firmware!
The only consequence is that, you'll lose all of your preset radio stations and you'll also need to do a Circle Calibration to reset the compass; but it's pretty simple to do... the 4R manual shows you just how to do this; I've done it plenty of times after having the battery disconnected while installing some electrical equipment!
I'm pretty sure that this is what's causing the trouble; the good thing is... you don't need to take it in to the dealership to correct it! Please be sure to let us know how you made out because if that was it, you just saved another one of our members from going back to the dealership! 'Best to you' transistor!
rig, Cheers