Could just be that the window came loose from the tab. That happened to me, and I had the same sound that you're having now. My guess is that it's just the arm that holds the window moving up and down inside your door loosely and clanging on other stuff.

Anyhow, I fixed mine by opening up the door panel and setting the window back in the track with some aquarium silicon. Then I used some marine bearing grease to slime up the tracks a bit, and voila!

Here are some pics: