If it's properly hoisted (I have a Harken Hoist), it sometimes doesn't let the top down all the way in the front. This is because as it touches the rear tub of the Jeep the weight on the straps is relieved to the point the front won't come down. There's a slight take on TJs which is why it doesn't come down perfectly level. If it's close in the front (a couple inches or less) try to lift the hardtop slightly with your arm from the drivers side and unhook the latch on your straps. Then do the passenger side the same way. Then you should be good to go.
Of course, if this isn't your problem, then take a few pics since it's hard to tell why the problem is happening.
If the top was sitting on a platform that was suspended from the ceiling, it should be ok. If not, and some other method was used to hang it, that may have caused an issue with it being out of shape. However, the more information you can provide (photos especially, and some of the top as it sits on the Jeep) will tell the story.
The OP said "I hung it from the rack which is bolted to the top from the rafters" which sounds like he hooked to his roof rack and hung it from the rafters. We need picks of that rack and the gap at the window. That would let us know if that or something else is that cause.
The OP said "I hung it from the rack which is bolted to the top from the rafters" which sounds like he hooked to his roof rack and hung it from the rafters. We need picks of that rack and the gap at the window. That would let us know if that or something else is that cause.[/QUOT