If it is back there it's got to be getting in around the rear window or tailgate.
Are you installing the window tailgate bar correctly and pulling the zippers all the way down?
Remove the trunk, the rear seat and carpet hit it with a garden hose and check inside. All it take is a little trickle to really get a carpet wet.
2003 TJ, 33" BFG AT, 2" BL, 2" BDS spring lift, Truck Lite headlights, Homemade sunrider top.