Looks like Cooper's reaction to his allergens (dust mites, storage mites, and flea saliva). After they go flaky, does he lose hair in that spot? Does he have thinning hair in general?
Does this coincide with any cleaning, moving, or going over to someone else's house? Cooper can't deal with any major dust disturbance, and I have to vacuum at least twice a week to keep his symptoms at bay. When we moved, he erupted in bumps for weeks.
We went through the same food trials and tests for months before finally getting him properly tested for allergens. I don't want to know how much we spent on cultures, antibiotics, steroids, mite medicines, anti-fungals, and prescription foods before getting him tested. I highly recommend it! Turns out that he had NO food allergies, and that's what we'd been primarily treating for! He's currently on his maintenance dose of allergy serum shots and getting fewer bumps at every breakout. We still use Benadryl and very low doses of prednisone.
Once you determine if he has any food allergies, get a high quality food and supplement with extra omega fatty acids until the flaky skin clears up.
Cooper's definitely getting fewer bumps now, but we're still waiting for all the hair to grow back…