I've read of someone having a window problem like that before. If I recall, it was fixed through some sort of funky reset that they were walked through by a tech. (I'm almost certain it wasn't a simple reset.) You'll probably have a tough time finding the post, but it may be worth searching. I'll take a quick shot at it, and come back to edit this if I find it.
Edit: Wound up searching quite a bit, but couldn't find it. Sorry!
There's one procedure where you hold the switch in the closed position for 30 seconds and that forces the system to re-calibrate the "closed" position of the glass...