Is the puffer a new addition to your tank? Or have you made new additions to your tank recently?
It could be ich. Take a look at the pictures in the Diseased Fish Thread.
spots that go away can also be ich....ich will come and go as the parasite goes thru its life cycle. Take a look at the photos of fish with ich in the Diseased Fish Thread and then also look at the post on ich in the FAQ Thread.