Something that may be completely unrelated...
Anyone else put the top back on? When I had my TJ, my gf drove it a lot in the summer... which gets a lot of flash storms here in PA. When she put the top on, she would zipper the back windows, but not put the vertical tab in the slot (the one that goes up and down behind the door). On more than one occasion, this caused a lot of wet carpet.
-X