Stolen from Northamericanmotoring
http://www.northamericanmotoring.com/forums/stock-problems-issues/221146-need-some-quick-advice-re-window-problem.html:
This is a common problem and if the manual reset does not work the car needs be reprogramed.
Manual reset is as follows.
1. Hold window switch down and continue to hold for 10 seconds after windows is fully down.
2. Hold window switch up and continue to hold for 10 seconds after windows is fully up.
3. Repeat Steps 1 and 2 one more time.
If this does not work the car has lost its memory for the windows and needs to be reset. This can be done by a dealer reprograming (approximately 2-4 hours depending on your car) or can be done with a computer, cable and the correct software. There are threads on how to do this in the Modifications>Electrical section but be ware if you screw one thing up in doing this your car could be toast and that could be a real expensive fix at the dealer.