The rear window motor is supplied power and ground by the Back Door ECU, which in turn gets signals from the switch in the back door, and serial data from the body ecu, which gets a signal from the switch on the dash. The power and ground to the motor are inverted to change direction, up or down. It is highly unlikely the wires in the back door shorted to ground. Unfortunately the most probably cause is going to be the Back door ECU itself, although I guess you could have a switch that is stuck. You could test the functionality of the tailgate key switch, and even the dash mounted switch. If they both test ok, that would leave the body ecu and the back door ecu. I don't know if you can disconnect "just" the serial data wire from the two ecu's, if you disconnect the entire connector you would be taking away power from the back door ecu, so you couldn't really test it, unless you somehow supplied power to Terminals 1,2 and 3 of the back door ECU. Then you could disconnect 1E1 and 1E2 at the body ecu and see if is still going down on its own. If it does, the Rear body ECU is toast.

Of course the easy thing to do is find a known good one to swap in for a test.