Wow, I say it's probably a parasite problem.... I know Betta Slave has experience with that, and she could probably give you some good advice on how to clear it up.
As far as I know, a natural remedy would be to soak his pellets all the way through in garlic juice.
what about your ammonia? I noticed you wrote down nitrites as safe and nitrates as safe.... I'm assuming this means 0 nitrItes and 10 or less nitrAtes, because any more of either could be dangerous.