did you touch any of the wiring or anything? i could possibly see if some wiring got shorted somewhere along the way, and the power for the lock got routed through the line for the window as well.. other than this, I'm not sure. does it go down if you lock the door from the inside while the key isnt in the ignition? does it do this if you lock the door using the key hole on the door? basically, is it only the remote that does this, or the act of locking the doors while the car is powered off? also out of curiosity, does it do that if you lock the doors by the remote while the car is running? and, does unlocking it cause anything to happen? I'm not an expert on this by any means, but narrowing it down may help figure out the problem.