>The unwanted output is of a different nature to the signal
>generated by hand turning. It's generally non-quadrature and
>'messy'. The signal shape and level at the stepper coils
>depends on speed. At a very low stepping rate, about +/- 300mV,
>kind of 'lumpily' sinusoidal, at higher step rates the voltage
>goes up to several volts and is much more sinusoidal

It sounds rather like you are seeing harmonics of the step signal. I 
remember reading an HP journal back in the 70's where they put a lot of work 
into driving a stepper assembly on a plotter with a waveform that had 
appropriate harmonics added to the drive waveform, in order to get maximum 
speed from the motors. It sounds to me like you are seeing the same problem 
in reverse. 

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