I'm having a somewhat similar issue. I just got the car in December and I've had issues with the "bounce back" feature of the auto up windows. For those that don't know, the windows are designed to go back down if they detect an obstruction when going up. My problem is that this seems to happen when the window just normally hits the top. I can't close the windows all the way because as soon as they hit the top, they bounce back down. I can get quite close to all the way up (to the point it is still water tight), but it's not quite a full seal. Here's the strangest part, at first this was only an issue with the driver's door. Now it's only an issue with the front passenger door. It moved! Its winter so I really have very little need to open the windows at all.
