I had the same problem with my 2000 vert. There is an easy fix and was posted some time back, so you may be able to find the particulars there. As I recall, the procedure involved removing the access panels on the inside of the door - one is the red reflector and the other panel is located at the front bottom of the door. Inside you will find adjusting screws which allow the window to be moved and to actually move the top of the window in or out. My window needed to have the top moved in towards the convertible top, and after a few turns of the adjustment screw, no more problem. Since I don't remember all the particulars, I'm sure someone here does and will give a more detailed description. Rest assured, however, that it is a common and easily remedied condition.
Ron