I wouldn't expect there to be a problem with the glass, unless it's the incorrect part. I just replaced one of my doors, and had to switch the windows since the scrap car door had tinted glass. Anyway the first time I put it in, it didn't align correctly somehow, and did basically what you're describing. I really didn't know what to do either, so I removed the guides and reinstalled, somehow fixing it. I also had put silicone paste in the guides, and lithium grease on the track. Sorry, that's all I've got.
