On stepper motors exist something called "[mid-band resonance][1]". This is due to the fact that at this speed the stepper behaves like a Spring Mass System. I found a good explanation about that written by @zebonaut [at this question][2]

Have you tried increasing the speed to see if the motor rotates smoothly again?


 [1]: http://www.geckodrive.com/support/step-motor-basics/mid-band-instability.html
 [2]: http://electronics.stackexchange.com/questions/11811/how-do-you-minimize-stepper-motor-vibration