How large is the tank? If it's a 220g that's not a huge bioload, but if it's a 25g it's an entirely different story! What type of lighting are you using, and how long is the photoperiod? You mention that some polyps are browning, lighting or water conditions could have something to do with it.
Saying 'all water tests are fine' doesn't really tell us anything, it's best to post the exact results. NH3 and NO2 should be 0, PO4 as close to 0 as possible, and NO3 should be as low as you can get it.
The brown stuff may be diatoms, it may also be brown cyano or dinoflagellates. Unless you can paint a full picture of the tank it's really hard to say.