Well i had that issue.. was the button at fault. $30 (aud) later and all fine. I knew it was the button as it felt funny for a month when pressing it.
If it's not the button.. could be the auto up controller on the winder (which means replacing it which is a pain). Or it could have remembered a different fully up position.
Try disconnecting the battery.. then winding the window down and hold for 15secs.. then wind up and hold for 15secs to reset the top and bottom position.
Yes... i'm a total car nut! Why else would I upgrade my mower to rev to twice its standard rpm!