Funny, I did this a few weeks ago and have the same problems with both the windows and the sun roof.After changing the battery out once, not sure I'll ever do it again, what a pain. When I got the new battery in, the negative pole was too slim and the clamp on the cable would not tighten down on it, even more of a pain.
I think my sun roof started working on it's own some how, but will try to solve the window issue tonight, hope it works.
