What kind of light do you have? I had a 55 gallon with a GLO fixture and my vvery bright green polyps looked brown underneath it. It did not affect the color of my green birdsnest though.
So they changed color from green to brown? I would suspect lighting or a sudden parameter shift. There is a variety of star polyps that are brown......I believe they are actually called "purple" by some folks. Here are some that I owned in that past --
Mine were also brown under 20k MH's. Never did figure out why they changed over. They were very healthy though so I never worried about it. I agree that they just might be of another type of Star Polyp and nothing is wrong with them or your water~