if the steps per were wrong it would still find its way back to zero, lost steps would make both work and machine coords to change together. I'd start by lowering acceleration and velocity by half and seeing if that improved the condition. Also check for binding on the axis or screw as well.
If turning them down does eliminate the lost steps, increase acceleration and velocity until it starts doing it again and drop it a significant percentage.
also check any couplers for tightness
John