I had the same problem. Check the two holes w/plastic bushings on the windshield frame that the two chrome metal pins go into when the top is up. The bushings are probably worn out and the metal pins are hitting the metal windshield frame. Replace those bushings or rig up a hard plastic sleeve like I did. Good luck.
Mine rattles also, it's just one of the many things you have to deal with having a vert. I've heard that the metal pins also come loose occasionally, so check those while you're at it.