I just dropped my '05 convertable (~700 miles) at the dealer to fix the same apparent problem. Whenever I would hit a bump in the road, railroad track, or driveway, I would get a clunk noise from the drivers side window. It described it as a glass to metal sound and it never happened if the window was down more than an inch or so. The service manager said he thought it might be the window motor mount being loose as that has occurred often on these cars. I pick the car up Saturday after returning from a business trip and can post an update on the results.