window closing unit not working

It was working until the battery was drained and I recharged the battery. My car is 2001 Civic 2 door. When I arm the alarm system, both windows and the sunroof will automatically close. Now only the sunroof still close properly, but both windows only go up 2 to 3 inches. That is everytime I arm it, they go up only 2 to 3 inches. Is the closing unit toasted or is there a way to reset it. Alarm: clifford intelliguard 7000; clifford closing unit 48-567.. By the way, the alarm and door lock work fine.Thanks.

When you charged the battery, what are the chances that you connected the charger or jumper cables up backwards?   This could have blown a fuse feeding the window module.  Have you used a volt meter to do any troubleshooting?  If so what all have you checked so far?

Check the window closer instructions, you need to do a reset.

what is the battery's voltage resting at?
it could be at a lower voltage, thus having to draw more current to close the windows, and thus the window module is thinking that the window is fully closed.
make sure your battery is fully charged, or as howie said, there should be some way to reset the unit.

THank you for all the replies. I bought the car used and there is no user manual come with it; therefore, I do not know how to reset it. I will search for a manual and is there anyone knows the procedure of resetting it. Thanks.