Some C-14 rotors have displayed a tendency to pulse or vibrate when the front brake is applied. Sometimes this is caused by either a warped rotor or a warped rotor carrier (the disc inside the rotor itself that mounts the rotor to the wheel). The only way to really address that problem is to get rid of the warping, either by straightening the warped part or much more commonly by replacing the warped rotor(s).
My first set of rotors was replaced under warranty with over 50K miles on them; they were indeed warped and new rotors made the bike brake as smoothly as it did when it was new. After a few thousand miles though I noticed the pulsing returning although it was much more subtle than it had been before. So I checked both front rotors and they were straight and parallel. The next thing was to try scuffing them with some 150 grit sandpaper to remove any contamination, especially any pad material built up in one spot on the rotors. No change at all after cleaning the rotors. I tried cleaning them a second time, this time using a drill mounted rust- removal pad, and they again act just like new. So it takes a lot more aggressive cleaning technique than a quick scuff by hand to get back to the rotor's surface. I was surprised at this because I did scuff the rotors until I could see a clear pattern of sanding marks that I thought would have indicated a clean rotor.
This is how I was finally successful in cleaning the rotors:
The pad is a fairly stiff paint removal pad, available at any hardware store for a few dollars. The wheel is sitting in a wheel balancing stand so it is free to turn. Start the wheel turning slowly and apply the paint removal pad slightly below center and the wheel will continue to spin. Sort of like a poor man's lathe. The pad is not really aggressive and will not produce sparks but it does quickly alter the finish on the rotor's surface and leave a dull sheen behind in place of the annular rings from the pads. There was no measurable material removed from either rotor using this technique. Of course the rotors need to be unbolted from the wheel and turned around to get to the inside but it only takes two bolts to hold them on for cleaning.
Brian