Hmmm....well, there are times when skin can get irritated from what's going on from the outside. But, since skin is an elimination organ - it often show what's going on from the
inside. SO, what are you feeding? Bc, there might be something in his food that is causing flaky skin. Is he itching as well?
You may also want to consider Eicosaderm, which is an excellent supplement for skin/coat and overall health (fish oil + vitamin E):
VetAmerica: eicosaderm