There is a really great Technical Service Bulletin that was released to the VW service departments that explains how to "calibrate" the Eos windows. This calibration was the prescribed solution to the "phantom window operation" that we have all come to know as "pinch protection".
Basically, the TSB described a process that would let the Eos know where the "top" position of the window should be in order to stop the windows from trying to close too far.
I will post the link to the bulletin, however, want to make two things clear first before I do.
1) Normally people don't have access to tech bulletins as they are supposed to be directions to service people. As such, some of the language found in the bulletins can be "technical" and hard to follow. If you don't understand the instructions, please don't try it. (read it through all the way first before starting and remember... Your dealership probably doesn't want to hear that you are performing service bulletins yourself).
2) I take no responsibility for anyone who "demonstrates" to their car that the fully closed position is only half closed.
If you mess up the process, just start it again... This one really can't hurt the car, at least, not when I did it to mine.
EDIT: Oh yes, and 3) Make sure you lubricate all the seals with the VW Seal Lube before starting. It is important that the seals around the windows all be nice and "soft". (I know, I said only a couple of points... sorry)
Here is the link: CLICK HERE