stupid question, but, you did install the plastic window surrounds after taking off the hard top right ?
I've experienced all sorts of soft top maladies before I got it straight.
first check that the rods that lay above the windows are correctly in the grooves of the window surrounds and they are pinned in correctly
second check that the plastic tabs are tightly inserted into the tub flange at the bottom of the rear windows. finally check that the from part of the rear windows are folded into a "U" shape and fit into/around the door frame.
It would help if you posted a picture of the gap