oceanist,
i'm not sure if it's cyano or if it's diatoms. but you might want to invest in a cleanup crew. i bought 3 small emerald crabs from exotic, and a little turbo snail, and they ate up all the brown stuff. the crabs are freakin huge now. i then ordered a clean-up crew from this site and they are taking care of all the other crap in the tank.
but other than that, there shouldnt be a problem with the animals in your tank.
also, you should get a calcium tester. dont put too much of the calcium additive. i heard that you should only put that if your inverts and corals are using them all up, and your rocks are turning purple.