Check the door wiring. They've been known to break. It'll cause funny things with the windows and doors, and interior lights. I saw a writeup in the FAQ.
Edit: Here it is: http://www.myturbodiesel.com/1000q/a5/wiring-harness-vw-jetta-repair.htm
Edit: Here it is: http://www.myturbodiesel.com/1000q/a5/wiring-harness-vw-jetta-repair.htm
