Something else I found that you might want to try...
"Start the car, put the window all the way down, then push and hold the button in the up position, when the window reaches the top and stops moving, keep the switch depressed for at least 5 seconds, at no point of putting the window up and holding the button after the window has finished, do you release the button. If you do start over. This will tell the window module where it is in it's travel.
You need to have the door closed while doing this."
http://forums.pelicanparts.com/showthread.php?t=435016