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I think my turtle has fungus on his shell. I can only see it under water it looks like the picture on this post but mine has more on the back of his shell viewtopic.php?f=5&t=27810
When he's out of water it looks more like a shell that is flaking off. Here's a few pictures of the affected areas.
When I touch it it feels different then the other part of his shell thats normal, but it's not really soft, it also does not smell bad.

So what caused this? Is it shell rot or fungus? If so how do I get rid of it and prevent it from happening again?

Here's the pictures of his shell completely dry and in the sun.

I can't tell much from those photos besides some irregular shedding. Do you have higher-res ones?

I'll see if I can borrow my parents camera tonight and take a few pictures. I don't know why he would be shedding irregular he has everything he needs to shed healthy, uvb, a some what good diet since he never wants to eat vegetables, and clean water.