Is the glitching at the same frequency? Is there one speed where its worse? I wonder if you're experiencing mid-band resonance where the mechanical and electrical parameters combine to absorb energy to the point where the motor cannot maintain enough torque and therefore loses steps. If you sweep the frequency can you determine a specific point where the glitching is worst? If so, try adding some damping to the motor shaft, e.g. a flywheel or some other angular weighting. Does it still glitch then and has the glitch point moved? If so this would indicate a resonance issue.