I've had the same issue. I mainly notice the flapping at where the soft top meets the windshield. Like the last person said, turning on the air with the outside intake on increases the pressure inside the Jeep and pushes the top up enough to clear the trim. I've also put my hand up there and gotten the same effect. I was going to cut a thin rubber tube in half and glue it to the trim to soften the contact point to see if it helps, but I haven't tried it yet. You may want to try pushing up on the roof at different points when on the highway and see if you can get it to stop and it may help you figure out where to add some padding.
Normal people believe that if it ain't broke, don't fix it. Engineers believe that if it ain't broke, it doesn't have enough features yet.
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