I had a heck of a time with skin fungus a couple of years ago. The hatchling redcheeks I got were constantly getting it and a few lost a couple of toes. Some African sideneck hatchlings I had got it too. I would treat with antibiotics and keep the water crystal clear but the fungus kept coming back.
Then I remembered an article that a friend did on matamata turtles. Despite feeding well in captivity, matamatas often develop horrible fungus or shell rot. But when kept in acidic water (like what they are found in)they thrive.
Once I lowered the PH of the water and treated with tetracycline, the fungus disappeared.

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