If you were having lighting issues, it may be from corals expelling zooxanthellae which almost resembles dinoflagellates. I think I had a similar issue at one point. When you turn off all pumps does it suspend in the water column? I ended up doing several water changes, each few days apart and spending hours sucking out what was suspended like that until it was gone.
And it still may have been dino's for all I know. But it went away fairly easily where dino's usually are very hard to get rid of, so that is my guess.