If its the front BUT your latral runout measues within spec off the vehicle, try measuring it on the vehicle. Could be the hubs not sitting on the bearing correctly or the bearings aren't set right. Had a similar issue. Pulled my rotors off twice and re machined them. The problem still persisted. Tried machining them while still on the vehicle just as a poke and hope. Viola! Problem solved.
07 KJ- 6 speed, 4 inch BDS/ Daystar lift, 35x12.5 m/t's, homebrew snorkel, muffler delete w/ straight pipe, way too many lights, and a loud system to drown out the JEEP noises.