You may have already done this but I didn't when we got our new TT last September. After a heavy rain I went out to make sure we did not have any interior leaks. Looked at all the windows and had 7 of 8 windows had some water in the track. I scheduled an apt at CW to have it looked at but I also went to each window and turned the knobs that open/close the window. All were a little loose and I could turn but did not think it was enough to fix the problem.
CW checks all windows and no leaks. I take it home and spray water all around each window myself and no water. No issues since. Might be a simple fix.
