When you say he was sick, do you mean he had an upper respiratory infection? Did the shelter treat it in any way, or did you when he came home to you again? URI's in the shelter environment are very, very common, especially with cats who are stressed. Perhaps he has a residual viral infection in his sinuses. Does he sneeze? Do his eyes water? Is there any discharge from his nose at all?

Cats, being prey, can appear lively and apparently healthy even when seriously ill because it's one of their defenses against predators. I think all of us on this forum have learned to look past good appetites, playfulness, etc. and focus on symptoms because we've all been fooled in the past.