Sounds to me like it might have been the mating surface on the stub axle that was at fault rather than the discs themselves?
I can't remember why, but I removed my discs about 15 years ago and when I replaced them I had a dreadful pulsing through the brake pedal as if the discs were warped. Double-checked the mounting and somehow I'd managed to trap a tiny bit of debris between the disc and stub axle mounting faces. Cleaned them up and flatted them off with a bit of emery cloth and some engineer's blue, reassembled and they've been perfect ever since.
This sounds a very plausible solution Tim although probably not an answer for everyone with disc runout issues. Machined mating surfaces between hub and disc need to be scrupulously clean and free from burrs or damage. Securing bolts should then be tightened in a diagonal sequence culminating in equal torque on each.
