Unless you have a pest, or an outside contaminate as people have mentioned I think your issue is linked to Zeovit. There are so many moving parts to Zeovit its really hard to pinpoint a problem.
I can only speak from my personal experience with Zeovit, I have used to twice, and when it is working it works amazingly well. However, I had similar problems as you had, even before stopping, which is what prompted me to stop, and when I stopped even when I tried to go even slower the second time, things got worse.
They way you stopped zeovit by simply not changing the stones, is really not the way to stop, you should slowly decrease the flow of the stones, and use less stones over a period of time. Zeovit uses say 4-6 weeks, frankly I think it should be even slower than that. As you do that you have to slowly decrease the addivitives.
The problem is as you do this things become stressed as you described, and parameters can be thrown even more out of wack. Decreased growth can lead to spikes in ALk, CA.
I found that I would have to weather the storm and minimize damage, keeping doing water changes, choose my new system I was going to run Carbon dosing, fuge, biopellets, ATS etc. Monitor your parameters especially alk, ca, Nitrates, Phosphates.
Test for Potassium as well, Zeovit consumed a lot of Poatassium in my tank which slowed to nearly nothing once i stopped. High K can lead to burnt tips and other issues.
Once my tank stabilized and everything normalized the sps healed and started to do well again. While I really liked the Zeovit results, there are so many variables to account for when something goes wrong its not that easy to pinpoint.
One thing I did which might not be an option was, I switched back to Radiums from my ATI PM, I still run T5s on my frag tank, but I found that the sps recovered better under the Radiums.