Did you THOROUGHLY clean the mating surface of the hub with a steel brush before installing the new rotors?

Also do you use tire foam? I have started seeing more and more brake vibrations as the result of this stuff. What happens is that a little gets through the wheel spokes onto portions of the rotor. It acts a lubricant that coats the surfaces on only portions of the surface changing the coefficient of friction as the rotor turns against the pads.

If you use tire foam, make a cardboard cover that fits the wheel and hold it in place as a mask to ensure that no droplets of tire foam make it to the rotors.