In reply to richyfenn:
It isn't the step size as this is a very posh stepper, it is a slight offset on the rotary axis.
Grab a tin and stick a finger in the middle of each end, holding it so it is lying on its side. If you rotate it with your fingers as pivots then watch from above it doesn't move side to side. Now do the same but with your fingers only 1cm from the edge; as it rotates it moves in an eccentric fashion. At two points in the rotation it is offset in the Z axis, 90 degrees either side it is offset in the Y axis and in between it is offset in both.
Basically someone made the jig fractionally too thin so the workpiece sits fractionally below the centre of rotation of the stepper shaft.
Problem is I need to write a very precise report which is both technically correct and also very hard for a layperson to misunderstand by a mix of guesswork and Google