I have seen the same symptom on other hondas and the cure was turning the rotors while still on the car. the new rotor itself may be straight and true but the hub assembly may be a bit warped, causing it to touch the brake pad as the rotor rotates. Ask the shop if they have an on car brake lathe and see if they will turn the new rotors with it.
also may not be a bad idea to have the bearings checked while you are at it.