I found myself in a similar situation situation: Upgraded from 4.2.2 (PDA: I9500XXUBMG1, CSC: I9500OLBBMF9, MODEM: I9500DXUBMF8) to 4.3 (PDA: I9500XXUEMJ8, CSC: I9500ODDEMJ5, MODEM: I9500DDUEMJ5). I already had CWM 220.127.116.11 on the device prior to this.
Changing to a SELinux disabled kernel did not work, and running su in a terminal prompt always returned 1. Flashing CF-Root via recovery or via Odin did not work too - always reports successful, but apps all fail to get root access.
After that, I did some poking around the filesystem and the SuperSU v1.65 CWM zip, and realized that the init.d script for the SuperSU daemon did not get installed correctly, because /system/etc/init.d directory did not exist. So I rebooted into recovery, mounted /system, created the directory via adb, and reflashed SuperSU, verified that 99SuperSUDaemon was indeed copied to /system/etc/init.d, then rebooted.
Voila, root access was back.
Hope this helped someone.