My guess is one of 3 things happened (at least that I can think of off the top of my head):
- The ROM has issues itself. Perhaps it wasn't rooted properly to begin with.
- Something got flashed that didn't work properly with the ROM, and breaks root. A kernel perhaps.
- Superuser and supersu both exist, and both lost the battle for root. Only one can be functional at a time. They both can be installed, just one has to take the backseat to the other. I personally find it silly to have both, and just stick with one or the other.
Are you flashing the newest one? Perhaps flash a different ROM. Perhaps a wipe of data, cache, dalvik cache, and system partitions is in the cards for you as well.