Your problem seems to be pretty common when a TJ is lifted. I don't know if it has anything to do with what brand of spring you use or not. My TJ, like yours, has Rough Country springs has some spring rub on one side. The axle/suspension/frame are all properly located. I even switched the springs side-to-side and the rubbing did not switch with the spring (I believe it's a manufacturing tolerance issue). You wanna know how I solved the problem? Chain Wax. You could also turn the radio up and achieve the same result. This rubbing won't cause any problems.
2001 TJ, 4.0 Liter, 3.73s, Rough Country 2.5 Suspension Lift, JKS 1.25 BL, JKS 1" MML, Advanced Adapters SYE/Tom Woods CV Driveshaft, JKS Quicker Disconnects, JKS Track Bars, JKS Control Arms, Aussie Locker Front (Dana 30), Dana 44 Rear w/Trac-loc, Rough Country Rock Sliders, Rampage Fastback Softtop, BFG A/T 33x10.50x15, Stock Canyon Wheels.