Just curious as to what your water parameters are and what test kits your using, how old? The palys look a little shriveled, which means it could be water quality. I just want to rule this out, as your other corals look fine.
I still think it's a nudi. That's almost exactly what a colony will look like after a nudi goes through it, and if you've had them in the past, you could very well still have them.
As for the puffer nipping, keeping him well fed is all you really can do, some behave, others don't.