Some people have been getting a problem where the power windows will work for 10 minutes after connecting the battery and then stop. The problem seems to be in the wiring harness and not the door controller on the power window motor. Look at this and the linked threads:
http://newbeetle.org/forums/2-0-liter-gas/73914-99-beetle-2-0l-possible-ccm-failure-confirm.html
Try disconnecting the battery for a few seconds, reconnect and try the windows. See if you have the same "works for 10 minutes" symptom.
http://newbeetle.org/forums/2-0-liter-gas/73914-99-beetle-2-0l-possible-ccm-failure-confirm.html
Try disconnecting the battery for a few seconds, reconnect and try the windows. See if you have the same "works for 10 minutes" symptom.