I have 2 threads about this issue, first they will tell you that you put the tops back on wrong, and when you fuss enough they will replace the seals. My 2012 JK has been in 5 times for roof leaks, to include 2 new freedom top panels. This last time they had the tech in to look at my jeep and 5 other jeeps. My roof seals have already been replaced 3 times and the door seals 2 times. I know the frustration, all I can tell you is demand the dealer fix it. Also a nasty review about the dealer works wonders, jeep takes the reviews they send to you serious.
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