if you have dead inverts in your tank, it will spike your nitrate levels.
where are the rocks from? they could be a source of phosphates/nitrates as well.
just because cyano is disappearing, it doesn't mean phosphates are leaving the tank. phosphates are held within the cellular walls of cyanobacteria and as it breaks down, phosphates are re-released into the water column.
remove the rocks, syphon out the cloudy water that'll disperse after you lift the rocks, then add new water.
try to keep the rocks from touching the sand the best you can so that you won't have detrius (aka poop) collecting near/under/below the rocks.
check to see if you see any dead blue legs in the tank. although they're small, decaying inverts will foul water rather quickly.