Can't Figure Out This Leak

[Polygon]

I just got my car back from the body shop for a second time and I've got a leak that wasn't there before it went in, in the first place. The leak is coming from the seal that seals between the window and the door frame. The seal looks fine and is soft and pliable. It seems the window isn't going up far enough. On the outside, when I push on the seal I can easily touch the top edge of the window. If I wash it the water will go right past the seal. However, the window is pushing on the seal. The motor seems fine, doesn't seem like it's having trouble, but for some reason the window isn't going up all the way.

Any advice?