I had the same issue early on and it persisted for some time. I did at lot of sand cleaning and eventually bought some snails that were supposed to clean it up but they did not. I now have a tiger pistol shrimp that is constantly building new homes in the sand and mixing it up so I don't notice it anymore. Recently I had a lot of red cyno show up on some rocks and sponges so I used Chemiclean twice with good results both times, but it came back and I am still fighting it. Now I have my PO4 at 0.02 and Nitrates at 2.5 ppm as of this morning trying to starve it out. Will probably turn my lights off for a few days next. I have a mixed reef, and I probably relaxed my cleaning schedule at bit and opened the door letting my nutrients get as high as 0.2 PO4 and 20ppm Nitrate. I started dosing NoPoX to keep them down now.
