Polyp extension can mean different things. It might relate to flow, respiration etc... Hard to narrow down exactly.
I would suggest investing in some quality liquid test kits for your alk, Ca, pH (or meter), etc. As far as your levels, I personally try to aim for natural salt water levels as opposed to higher than natural salt water levels.
Here are some ranges for your levels you should aim for:
Reef Aquarium Water Parameters by Randy Holmes-Farley - Reefkeeping.com
Browning out can be attributed to different factors as well. Higher nutrient levels in the water, low lighting, lighting in the improper spectrum are going to be the main causes I think in brown sticks.