My sister had an '00 New Beetle sedan for 5 or 6 years and had several power window failures (and other electrical issues with interior bits).
After making a scene at the dealer one day, they contacted VW and she got the windows fixed and they worked fine the last two years she owned the car.
She wanted to get into a Jetta, but just couldn't deal with any more electrical problems and long VW indifference (although her dealer did improve a bit after her rant in the showroom). She wound up with a Subaru. Sounds like VW was still having issues in '05 with the windows.
Try contacting VW for some after warranty assistance.
The Secret Warranty