I know OP has sorted his problem, but as its so common & this is one of the first threads to come up on google, here's a clue for new visitors:
Remove motor casing (Flattened cylindrical cover wih 2 bar magnets inside), rotate thru 180 degrees & refit. This will reverse the motor direction & sort the problem. Switch & motor now operate in the correct sense, including the short "drop" on door open & "lift" on close.
You may need to recalibrate window top/bottom stops after refitting: Wind window to top, release, hold "up" buton for 5-10 secs. Wind to bottom & hold "down" for 5-10 secss. Sorted (Well, it was on my '01 TD4 anyway)
HTH
Plugs