I just noticed that my weather strip is torn on the inside in the hollow section. That could be why the weatherstrip is not touching the top of the window correctly. The driver side is torn too but not as bad and the window is adjusted perfectly. I think my leak is caused by a combination of problems... the window pitch needs an adjustment and the weatherstrip is not pressed tightly against the window.

I bet the guys that replaced my headliner tore my weatherstrip! I am thinking about stuffing the hollow part of the weather strip and checking to see if water gets in.