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I don't have any rattles with my windows up or down. I actually think the top does a pretty good job of minimizing road noise. I do need to get my windows adjusted, if I raise by front windows first before the rear quarters are up I get a clunk.
You sure it is the window? On reason i say is i notice if i put anything in the little cubby's on the door that they rattle with the bass of the stereo.
I have the same problem with a 2006 vert. Like mlawdag, when I roll the window down, even a bit, the rattle goes away. I've had the car for 3 weeks and just noticed it a couple of days ago then saw this post. Not a huge problem but would also like to know if any others have this with their verts and have fixed it or can suggest fix. Thanks.