Do you have your ZEO reactor programmed to come on for 3 hours, turn off for 3 hours, etc etc? I found that to be absolutely vital in my system.
No it runs 24/7 the on off is when you are adding zeo to a existing system with corals i belive. I did zeo from start up. I've worked with Alexander the top guy on the zeo forum to fine tune my zeo system and it was said to have my reactor running 24/7. This might also be because of my high fish bio load.