Is there any redness or swelling in addition to the flaking?
My brother had a cat that had Plasma Cell Pododermatitis. It took a lot of tests and a long time for the vet to figure out what was wrong. Basically, they won't find it unless they are specifically looking for it. They had to do a biopsy of the paw pad to figure it out.
It started off with flaking pads, then redness and swelling which eventually left the cat nearly unable to walk. It was easily treated with Doxycycline and cleared up completely.