the biggest difference, with regard to diet, is that most who follow paleo totally eschew dairy, whereas we feel that if you can tolerate it, no harm no foul. some in the paleo camp feel that rice & white potatoes are pretty okay too, so long as you don't have weight to lose (mark recently talked about this). on the other hand, paleo generally refers only to diet, whereas primal encompasses most aspects of your life - stress, activity, sleep, etc.
hope that helps! if your doc wants you off dairy, that's probably why. it's also possible, however unlikely, that he's never heard of the primal blueprint. most who find one hear about the other.