Thanks to Gene Heskett and Chris Radek for their help. I must have picked up an electrical noise problem in the index pulse since I last checked because it's giving two unequally spaced triggers per revolution of the spindle at the moment. This, in turn, puts an unrealistic jump in the encoder velocity signal. I could have sworn that I confirmed a clean signal coming from the encoders but I must have been wrong. Leave it with me to clean up my electronics and thanks again for the help.
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