A dip like that most certainly would've lowered his immune system. I'm betting what happened was that the IP's were always there, but it took an immune hit to make him unable to deal with them. You're treating, then reinfecting. Because he never gets a chance to bounce back, he's just in a constant state of illness. The rays have never been fully treated, so there is the reinfection. Just an educated guess.
Again, I'm no expert. I'm in the medical field, but not fish medicine. It just makes sense. That would be the case with other animals, humans included, who were subjected to parasites, so it stands to reason that it would be the case with the fish.