There are three stages of the ZEOvit system... Stage 1 is just starting out fresh with a new tank (where you were). Stage 2 is when your system is running ZEOvit but is not ULN yet, or established tanks just starting ZEOvit. Stage 3 is when your system is running ZEOvit and is a stable ULN.
You are in stage 2, so please keep that in mind. As you started your tank with dry rock, it’s likely you will be in stage 2 for much longer than if you had started it with live rock... this has been my experience at least. It’s not an issue, it’s just extremely helpful to keep this in mind and adjust your system accordingly.
It is recommended that you alternate between 3 hours on and 3 hours off all day every day when you are running ZEOvit in a nutrient rich environment.
What is your dosage of ZEOvit media (sorry if you already said and I missed it)? As you are in stage 2, you should be running 1 liter or ZEOvit per 150 gallons net water volume.
That's so strange about the reactor being on and off at 3 hours intervals. It's not that i don't believe you but having started my tank following Alexanders instructions when the Zeovit community was fully aware of my set with live sand and dry rock this is news to me. If i did this reactor change this wouldn't spike my po4 and po3? I am using a few rocks over a half of bag to cover my 55 gallons. I also have the flow adjusted to the correct flow rate. I'm sorry i do not remember that number off hand, i'd have to look at my thread on zeovit forum... If i had to guess i think i was around 60-65 gph.