http://www.drsfostersmith.com/pic/ar...=1046#answer_1
I'm willing to bet that if you look, there are what look like little "ulcers" or moist patches w/ slightly yellow discharge around it. Are there? They're usually quite tiny.
The flakes I saw looked and awful lot like what one of my Black Russians had.
It's a dietary issue. The symptoms were identical in every facet.
I'm just offering my experience. Otherwise (I didn't check) if you haven't already done so, I'd get an allergy panel done up on your pup. Further, they can draw blood and check and see if he's showing any vitamin deficincies. That's why I posted the link above to kinda show you some of what is recommended as a daily intake and that he/she might be lacking, or getting too much of.
The diet(s) you're feeding him may be high quality kibble, but somewhere he's either getting too much or too little of what his particular body needs!