The sensor in the frame is the one that tells the BCM to lower the windows, since your windows go down automatically, that one has to be ok in your case.

Another one is in the roof on the passenger side, the one on the trunk (that is probably the problem) and the one in the roof are wired in series and BOTH have to close to tell the hydraulics to run.

To find the one on top, unlatch the roof and push it up, go around to the passenger side and look up into the frame above near where the 'right eye' of a passenger sitting in the seat would be - look at the folding frame, there is a little switch there, it is there to tell the hydralic pump it's ok to run, since this switch can only activate if you have pushed the top up away from the windshield frame. Check to make sure it hasn't fallen apart.

It's usually the switch in the trunk, tho.