It looks almost as though it could be an allergic reaction to something. If he did indeed have mites, he may be reacting to the bites and hence the red swelling underneath the scales. It's really hard to tell from just a photo, but I'd seen a few similar cases that turned out to be an allergic reation to bug bites and/or medication while working at the vets. The only other thoughts I would have would be if it were at all possible that those scales had been damaged enough that they'd actually been pulled up a bit.

I would get a second opinion though if you're not confident in your current vet's diagnosis. Especially if it is a reaction to medication... Do you know when the marks first appeared?