Another consideration for flow is the placement of your powerheads. I keep mine 3 inches below the surface so my SPS get a nice blast but my LPS down at the bottom get low flow.With you saying that, I am thinking flow might have been the issue. I was running the reef wave on random wave up to 50% strength. The MP40 although new, I was running it on reef crest at 50%.
I have lowered the Reefwave to 30% on random, and the MP40 to 20% on Tidal Swell.
What program do you run your MP40s on?