have you tried resetting the windows to see if that helps? if not, worth a try (copied from another source)
- Sit in the car, and put the key in position 1, so you have power to the windows.
- Push and hold down the window switch, and keep it held down for 5 seconds after the window is all the way down. This re-sets the memory, telling the motor, in effect, "Remember where we are now? "
- Roll window back up, and release switch.
- Open door. Marvel at the downward motion of the window. Repeat on other side, if needed.