I know this is reviving a dead post but because nobody else had commented and the OP didn't provide any news about their eventual solution, I thought I would post the following:
I had the exact same problem. This is how I sort of fixed it (to save me the trouble of taking the door panel off and playing with the motor unit).
First, make sure the seal is properly seated inside and outside the door frame when the window is down - when viewing the top edge, there is lip hidden by the external rubber that you can expose by gently reflecting it - make sure it's under the metal frame of the door.
When viewing from within the cabin, there is a rubber seal that sometimes gets pinched in where the sliding window meets the triangular window at the top, make sure its out the whole way around.
When everything is in it's proper place, there shouldn't be in small indentations for ?pinches ?welds visible on the metal parts.
Second, use something soft to fill some space at the top of the window. I used some surgical rubber tubing that is around 12mm dia but compresses toe 8mm dia. I suspect an extension cord power might work just as well.
I cut a section and placed in at the top of the window where the glass would normally nest from front to back.
Third - window pinch reset. Not much could be found specific for skoda, but the VW instructions didnt quite nail it but I sort of ham fisted the following solutions.
Press window down completely so it returns to bottom position. Press bottom down button 3 times (you will see it retract a little bit more)
Next do full-auto up. It will hit the rubber tubing/power cord obstruction you placed and then auto retract half way
Hit auto up again - same thing
Hit auto up again - this time it wont auto up and you will have to hold window up to make it reach the top and it will stay.
When it is staying in the up position (with your finger holding it up) ensure the window is at a point that will allow your window to seal from weather but not push the seal/trim up too high.
At this point - quickly release and pull up on the window button a few times (like 5 to 20 times).
Afterwards - the window will fail to respond to button inputs on either the door or the master switches on the drivers panel - this is a good sign don't panic.
If it doesn't "lock out" of user inputs, repeat the above procedure a again with more spamming when its in the new top position (you'll often hear the motor click without movement)
I believe this lock out period is when its resetting its limit.
Once it's failing to respond, remove the rubber hosing / cordage that you put in to limit its excursion.
After a 3-4 minutes, the window will start to work again and should now stop at the new limit set - ensure you get full weather sealing.
It took a few goes for me to get the right amount of "Gap" set but its now good enough that it doesnt look faulty. I can still see the small "+" sign on the B pillar window column but at least the top edge of the glass is no longer exposed.
Hope this helps someone!