First off make sure you close the glass first, then the tail gate. The tail gate is what locks the glass in place. Also check the bottom of the glass for a rubber strip that runs across it. That is the seal, the tail gate when it closes pushes against it, to hold the glass down, and to complete the sealing process.
Also if memory serves me, there should be a pair of seals on the bottom of the hard top, where it meets the tub/body of the jeep to seal that joint. And another across the top of the windshield frame. They often get damaged on removal of the top.
You can pick up the top seals from places like Quadratec.
97 Sahara, 74 Renegade, 72 CJ5, 55 Willy's (the Beast) Boss 302, 6:34 gearing, Bose 901 speakers.
God I miss that Jeep. Forgot the kinda Jeep, 80 SX4.