As an actual owner of a JK, I haven't experienced any issues like you describe. I have the dual top option and run the Freedom top most of the time. Mine doesn't leak or have any unusual wind noise. All I hear is the soothing sound of the mud tires humming along. I just recently completed a 3500 mile trip in mine with no issues at all. If it were me, I'd take off the freedom panels, clean and inspect the gaskets and reseat the panels. Check all you bolts holding the top on to may sure they are snug. If that doesn't do it then I would start hitting up the dealer. You may need to take the tech on a test ride so he/she can listen for the problem. My wife had a rattle in the A pillar of her Escape that took three test rides with a tech to finally track down the problem. Good luck!