The question I have is when is the last time his filter was cleaned. If the bio chamber has been un touched for a long time it can also grow bad bacteria that can migrate into the tank. Substrate did not cause this as wild rays live on rocks, sticks, and who knows what else. They could probably live on sand paper if they had to, well maybe not that extreme. If there are other rays in the system I would bet they are showing similar signs. If it is the bacteria type I mentioned then they might or do have it as well. You won't see it on there backs, it shows up in feet, under disk, and tips of the tail. The ray usually is dead before you see it on the back side.