Could you give us the readings for ammonia, nitrite and nitrate?
The nitrogen cycle is an ongoing process in your tank. It is what prevents the water from becoming toxic. You should never see ammonia or nitrites above zero in an established tank.
You mentioned rocks - are they live rocks? or decorative?
You could try blowing the brown stuff off with a turkey baster (preferably one designated for fish tank only).
Any inverts in your tank, like snails, hermits, shrimp?