If you stuck rock in there recently, I would check for ammonia and nitrites. It's possible there is some re-cycling, that could be a big issue for a puffer. They don't do well with disease or bad water quality. You could post your exact levels if you want people to chime in on whether there cold be other issues (ph, temp), and also make sure there isn't a stray current in the water.
Ruling all that out, I suggest you watch for a few days before doing anything else. My (porc) puffer can lay on the sandbed all day some days, other days he's up in everyone's grill. If yours goes a day or more without food, that is definitely not good. I wouldn't worry about it otherwise, as long as you don't see anything external (white dots, slime coat problem, flukes, etc).