This will happen to every VW/Audi eventually. Mine does it all the time, I've learnt to live with it.
Here's what the VW tech told me:
The window has its own computer and will log the fault, to reset it press the button and hold it down till it's at the lowest point, hold the button for more than 10 seconds at this point, do the same pressing up. Also apply lubricant (wd-40) to the runners.
It worked the first time I did it but hasn't since. Worth a shot because he said to fix it permanently would be a couple of hundred pounds (not worth it IMO).