This is why I'm concerned with that, what your describing sounds a lot like this:
(courtesy of humblefish)
Uronema marinum:
Symptoms - These are the red sores often seen on chromis damsels. The disease seems mostly confined to damsels and clownfish, but I have seen some exceptions to that.
Treatment options - This is a very difficult disease to treat. Possible treatment options include: Metronidazole (ex. Seachem MetroPlex), acriflavine (ex. Acriflavine-MS), Chloroquine phosphate and copper. The problem is the fish can never be returned to the infected tank from which it came. Uronema is a “free living” parasite which does not require a fish host. So, going fallow will not eradicate it. Most fish seem protected from it via their natural immune system; but for some reason, chromis and some other fish are not always afforded this protection. Once a tank has Uronema, it must be assumed that the disease can survive in there almost indefinitely.
Formalin bath or freshwater dip may provide temporary relief for Uronema.