I don't know if this helps seeing as I've never had a carpet anemone. Mine BTA when first introduced would look great one minute and then next hour would be all curled up. This lasted for a month. The whole time my percs would wait til it would open back up and then go swimming through it again. At one point they were even pulling something from it so it appeared. It's three months now and the darn thing is taking over my 30 gal tank. It only closes once a week or so now. For some reason it just needed more time to adjust to the water or something. As long as your clown doesn't appear to be damaging it and it goes back to normal within a couple of hours I would leave it be and let it adjust.

Angie