I have a similar problem with the window. Turns out that there is a 2 pin motor and regulator fitted to my 16v when it should be a multipin one.
The controller board has been fixed to the 2 pin motor so like you say it only goes down in small intervals. This is was very annoying as it meant it didn't go up with the total closure on the car. But then it packed in completely.
It could be a similar thing on your car mate. Best thing is to get the door car off and have a look. Its quite easy to get the door cars off on the Golfs.
