Security System/Keyless Entry Problem

Does anyone know of a random problem with the 2001 Xterra Security System. The security systems has activated a kill switch in my car at random (Twice) so that when I unlock the door to get in and start my car it won't start. There's a blinking light by the "HAND BRAKE" which I am told is to hook a line to the dealers diagnostic computer and a blinking light indicates a problem. Dealership thinks its the security systems but can't figure it out. They seem to think I locked my car out of sequence... Don't know how I could do that, I close the door and hit the lock on the keyless entry button. Any ideas?