I have a 2001 super crew that has a slider. Ive owned it for 5 years and my window leaks at both sides. Not all the time, I replaced it 2007, it still leaks in the same place. It comes from under the plastic parts. Ive heard that it could be the seem on the cab, I live in Seattle area it rains alot, so my windows fog up from water getting in. Drives me nuts, It was installed by a glass co. Is this happening to anybody else.

 

I would contact the glass company that replaced the glass. Sounds like something didn't seal properly.