Its a known problem.
I wish you luck with the Scotchbrite. I had my front rotors replaced under warranty on my '07 GS. The same "judder" returned after the warranty expired. I replaced these with Galphers wave rotors and Galpher pads. Just like the OEM rotors, these too are behaving in the same way as you described. My wire wheels seem to be true and the mating surface of the rotor to hub seems to be normal. I don't know if its the mounting bolt configuration or if the wire wheels are the issue.