Most of the ones I've had in my tanks were brown.
My new setup has had clear ones popping up though. I'm positive they are the same since I've had the same live rock and same stuff in it for two years almost now.
I think I have a very very nutrient poor system now (barely feed the tank, way oversized skimmer) and they don't get anything to eat ever and therefore are now clear and tiny instead of brown and bigger like they were.
Just something I suspect, no way for me to prove it, probably a big fat brown aiptasia will pop up tomorrow.
Anyhow I think the color is just like otherthings in the sea, changes under different conditions, smae species of corals, even same colonies are different colors under different conditions.