Try folding the fabric a different way when you put the top down. I've never had that issue before. But I know that how you fold it as it drops can make a big difference in how flush it rests against the back of the tub.
'92 YJ - heavily modded
'96 ZJ - heavily modded
'05 KJ CRD Limited - 370 lb./ft. from a 4-cylinder and trail ready. Pure awesomeness.
'11 Mango Tango JKU Sport - Mods
'12 Dozer JKU Sport S - 6-speed - ACE rock rails - Max Tow package - Daystar spacers - 33x12.50 Duratracs