Wow, I just finished asking my vet about this the other day! It's blackheads, or build up from too much oil secretion. Nothing to worry about unless it becomes red, and looks infected.
Has the vet considered a fungal infection? My cat has recently had ring worm, which is a fungal infection (not actually a worm) and it causes raw, scaling skin. It seems to have effected his paw pads, so maybe it's worth looking into.