That shouldn't be the problem. Dirty flashing the ROM should give you superuser from ROMAny help here? I even tried flashing SuperSU but the install fails in TWRP. This is driving me nuts.
Could it be because I had flashed SuperSU on PA 4.5 BETA4 before I flashed 4.6? If that's the case, how do I revert back to Superuser?
I've already nandroid restored back to PA 4.5.