Originally Posted by andrew_b
It does sound like you may have a high thickness variation (TV) of the brake material on the rotors (the "transfer layer")that can result from not properly bedding in the pads to the new rotors. This can continue to get worse, as the pads continue to deposit more material on the "high spot" and skip the lower spots, much as a small dip in a road can quickly become a pothole.
Bingo. Although, an improper bedding isn't always the root cause of inconsistent pad deposit.
Either way, trying to re-bed the pads/rotors probably won't do anything at this point, it's already too late IMO. It would be like trying to get the flat spot out of a tire by doing a burnout = not gonna happen.
The only way that I've found to get a "high spot" out of a rotor caused by pad transfer is to swap the pads with aggressive race pads THEN do the bed in process with those. The Cool Carbons, or any other street pad for that matter, will not be aggressive enough to "knock down" that high spot given their rotor friendly compound. After the high spot is gone, you can switch back to your street pads. Do this (good idea if you have race pads laying around or can borrow a set), machine the rotors (terrible idea), or buy new rotors (only other option).
Just my $0.02