How did you install the glass? Did you use the correct mastic and put it on correctly? Did you install the thick rubber seal propperly? I recently replaced my windshield frame and glass. I followed the instructions word for word, and it still leaked. Putting on the mastic was the most miserable thing I ever had to do to a Jeep! It's stiff and requires a heavy duty caulking gun. If the mastic isn't applied just right it won't make contact with the entire glass surface and it will leak.
To fix it, I removed the thin rubber filler strip and loaded the void between the glass & frame flange with RTV sealant and re-installed the trim piece. No more leaks.