Like Angie said make sure all spots have water movement, lots of rock can cause those dreaded dead spots. I have some in my tank and it hasn't even effected my nitrates, but they are a bad idea, avoid them. Is your rock cured? Did you take it out of the water? On uncured rock there is alot of die off that can cause your nitrates to go up, so can taking the rock out of water. Water changed will help lower it.