I have had great success using Acriflavine to cure my fungal problems in Fly River Turtles. The worst one was treated with ketakonazole by an exotic vet in Newburg, N.Y.I have noticed that when I use fresh fruit such as kiwi, and romaine lettuce, any of the 'debris' left in the tank seems to increase the chance of fungal infections. Clean water with the right temperature is a must. I have kept mine at 81 degrees F., and use three mechanical filters, and a wet/dry on the tank.
I would STRONGLY recommend having the turtle seen by a competent reptile specialist.

Uuno