I have crank windows and a couple bolts that hold part of the window frame in were somehow missing, so it wouldn't shut all the way. I took the door apart and figured out what the problem was eventually. The window would come off the track and make that same loud noise you described if you tried to roll it up. Sounds like one of the tracks or guides is messed up. I could pull my window up w/o the crank but it wouldn't sit correctly. Should be a similar setup with yours but a motor instead of a crank. Good luck.