Not sure about the royal gramma - but, my clown fish lay on the bottom of the tank and I've had them for about 9 months. They're pretty healthy. I also just got a mandarin that lays on the sand motionless all night. The next morning at lights on he's got sand on him. At first, I was a little afraid but once the lights come on he perks right up and starts hunting for food. I would assume yours is okay, especially if he just does it at lights out.
If you acclimated him correctly, he's eating, and your numbers are okay - I wouldn't worry.