Skipped Steps wont Go Away

[RayStoner]

Insufficient power supply filtering is a common source of missed steps.

Make sure the power supply for each part of the system is bypassed with good quality capacitors. Place the caps as close to the devices as possible. Low ESR caps are better than ones that aren't. If you suspect high frequency noise could be part of the problem, use a 0.1 uF cap in parallel with the larger capacitor.

what voltage are you running the system at? Are the supplies regulated or unregulated?

Check your grounding.

Check your wiring, make sure that control signals are as far from high current signals as possible. If they must cross, make sure they do so at right angles, and don't lay side by side.

Are you microstepping? Have you tried changing the value?

You could try slowing down the acceleration and max speed too.

Does it skip more/less at any particular feed rate? during accel?

Is there any binding on the machine? does everything move smoothly, with no change in force across the entire range of travel? Does it move with very little effort?