After flashing the latest beta (beta 2), I had issues with SuperSU as well. My built-in superuser kicked in, so I didn't lose root, but Titanium Backup didn't register with SuperSU. I ended up going into CWM recovery and reflashing SuperSU manually.
When I rebooted, my superSU was gone, and I had to reinstall SuperSU. Afterward, I went into SuperSU settings and converted SuperSU into a system app. After downloading the custom backup script as instructed, SuperSU works fine. Superuser works too.
I should note, I decided to manually install PA 4.3 Beta 2 by downloading it through the Paranoid OTA and then manually flashing it in CWM recovery after wiping cache + dalvik cache.
