Perhaps he has developed a sensitivity to something. Between raw, kibble, and supplements he is eating a lot of different things during the day. It could be that one of those no longer works for him.
If it were me and the vet ruled everything medical out, I would cut everything out. No supplements. And just pick raw or kibble and stick to it for a week or two, that way you can pin point exactly where the problem lies.
I wouldn't be so quick to brush off the simpler possibility. Dogs can be very sensitive, what works one day may not work the next.