Sounds like the rotor problem we have in the Civic...
Good Japanese rotors don't suffer much from warping, but the surfaces will develop high and low spots. If the high spot is small and "not very high," the pulsing effect (in the case of the Civic, severe enough to make you want to get out and walk when the brakes are applied between 70 & 80 mph) will only be felt where it creates a vibration at the right frequency to set up resonance.
I'd try the spare set of rotors.