When you took the hard top off did you install the small 6" long brackets on each side of the tail gate. The look like kind of like this [ .
the rear window should have a rail on the bottom that slides into to those c looking brackets and then when you shut the tailgate it holds that rail in and seals it up. I know with my TJ you have to take those brackets off when you put the hard top on and I always forget about them when I install the softtop.
You can see the bracket on the back of this jeep on the right side, above the tail light (the black bracket)