What brand of rotors did you go with and did you torque the wheels down evenly and consistently? Provided everything else is right you can try cutting the rotors or seeing if you can get the vendor to replace them, and if they do I would go with a little better brand if at all possible.

I have had customers come in for brakes and then go get tires at the tire store and boomerang back to me because of brake shimmy. Grab breaker bar and torque wrench, walk outside, break loose and retorque their wheels, test drive, problem solved, and customer is happy again.

Back in the day of warranty buy backs over just this kind of crap they had us indexing rotors to hubs, what a nightmare. You were expected to take the rotor off, clean the hub, torque down this flat inspection ring, measure the hub and if it was withing specs (usually was) then locate the low spot and mark it. The new rotors were supposed to come with a dot on them indicating the "high" spot and I think you were supposed to juxtoppose them. At any rate they still expected you to put the rotor on FIVE different ways to find the combination with the least amount of runnout. Did I mention what a nightmare? Oh, and it was warranty time and it payed no more time that it did to just hang a set of rotors. Care to guess how many of those really got done? The spec on it was .3mm at the hub.