I had a similar problem several years ago - turned out to be the GM3 module. See post #28 on this link:
http://www.xoutpost.com/bmw-sav-foru...stumped-3.html
I stripped some wires on a cigarette lighter adaptor to get 12 volt power and confirmed that the window motor and regulator was fine (if you have already disassembled the door panel it's not hard to supply power directly to the window motor). The link above makes reference to the GM3 module repair service that I used. With rapid turnaround service I think I was without the module for only 3 days or so. Be aware when the module is out of the car the windows, wipers, and remote lock/alarm will not work.
Good luck - hope the above helps.