I know this is a dumb question but you did check to make sure there isn't anything in the "cubby holes" in the door right? I took mine in the other day because it sounded horrible with bass, I figured it might have blown out or something was loose in the door. Mechanic looked it over and was going to take the door apart and see what he could find. 20 minutes later he came back and showed me the tire pressure guage in the compartment in the door.
The dealer put it in the side door compartment and I totally forgot it was there. Needless to say after it was removed the horrible rattle went away.

Most embarrasing thing I have had happen in awhile!
If it's still under warranty maybe the dealer could take a look and firm up anything that is in the door and loose.