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I had a set of EBC discs once that were so out of true I thought a wheel was out of balance; except it only happened when I braked. Never had that with any other disc so wouldn't use them again.
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The instructions say they're very sensitive to the runout, and say if there's more than a tiny amount rotate the disc round one hole & repeat until the runout is within spec. They also make a lot of fuss about cleaning the hub surface to make it true. I get the impression if you don't get this right they're much more likely to warp which is what sounds like happened to yours.
Anyway, will give an update when I've mine on the car... hopefully I won't have the same problem you had!