I have a 94 jetta and it has automatic windows and the drivers side window and the rear drivers side window do not go up or down. When I bought the car the rear window didnt work but then after a couple months the drivers side stopped working. When you try to put up the drivers side window it sometimes makes the alarm go off. I also put in a cd deck and think that maybe some wires got crossed and that is why the alarm is now going off when you try to put the windows up?

SOURCE: 94 vw jetta would not start

I just experienced the same problem and it turns out its the timing belt. I've never heard of this before, but when I pulled the cover off the belt was broken. Not sure if any other problems exist (still need to make the repair), but thought I'd share.

SOURCE: 2006 Jetta TDI Electrical!!!

There is a known issue with the wiring harness in the doors. It's possible that the passenger door also has a bad harness (assuming they swapped out the one in the driver's door) Is that a correct assumption? It may still be related to your original problem too. I've heard of disconnecting the battery for 20 minutes to reset the electrical (door switches). You should def give that a try - it's free.
Also check out the forums at www.tdiclub.com - those guys know their VW TDI's...

Testimonial: "The battery disconnect did not work but I am glad to hear it's not just me."

SOURCE: car clicks when trying to start

When you try and start the vehicle does all the lights and radio and stuff go off? And does the starter make any weird noises when you try and start it? I would go to the parts store and ask them to check your battery if you can drive it there. lol..........they will be happy to check it out for you. Still acts like it could be a battery issue.

SOURCE: 1999 VW JETTA anti-theft alarm keeps going off & car won't start

pop the truck and the alarm will disable

SOURCE: need to reset manufacturer alarm on 94 jetta

turn the key on for 20 min. then try this has worked for me