From the pros at StopTech
In fact every case of "warped brake disc" that I have investigated, whether on a racing car or a street car, has turned out to be friction pad material transferred unevenly to the surface of the disc. This uneven deposition results in thickness variation (TV) or run-out due to hot spotting that occurred at elevated temperatures.
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Regardless of pad composition, if both disc and pad are not properly broken in, material transfer between the two materials can take place in a random fashion - resulting is uneven deposits and vibration under braking.
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There is only one way to prevent this sort of thing - following proper break in procedures for both pad and disc and use the correct pad for your driving style and conditions. All high performance after market discs and pads should come with both installation and break in instructions. The procedures are very similar between manufacturers.
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The obvious question now is "is there a "cure" for discs with uneven friction material deposits?" The answer is a conditional yes. If the vibration has just started, the chances are that the temperature has never reached the point where cementite begins to form. In this case, simply fitting a set of good "semi-metallic" pads and using them hard (after bedding) may well remove the deposits and restore the system to normal operation but with upgraded pads. If only a small amount of material has been transferred i.e. if the vibration is just starting, vigorous scrubbing with garnet paper may remove the deposit. As many deposits are not visible, scrub the entire friction surfaces thoroughly. Do not use regular sand paper or emery cloth as the aluminum oxide abrasive material will permeate the cast iron surface and make the condition worse. Do not bead blast or sand blast the discs for the same reason.

The only fix for extensive uneven deposits involves dismounting the discs and having them Blanchard ground - not expensive, but inconvenient at best. A newly ground disc will require the same sort of bedding in process as a new disc.