Stepper motor waveforms
At high step rates, step motors exhibit a dynamic instability.  In many cases, it results in a lightly-damped velocity transient.  That is what you are seeing.  In worst case, the drive will go unstable...loss of synchronism.  The reason for this is that the motor is a fourth-order non-linear system.  It cannot be looked at as a linear system!  The inductance and back-EMF definitely affect the stability.  In general, the higher the step rate, the lower the stability.  Believe it or not, the effective winding resistance (seen looking back into the driver) is the controlling factor.  An analysis of that is not something that can easily be presented here.