Problem found: the pulley wheel on my X axis had play in it due to a loose grub screw. This was causing a very small delay in the X axis responding to moves, I guess a bit like inconsistent backlash. Thanks for all your help on this, I really appreciate your input.
On a hardware note, I have nema 23 steppers with 3/8 d shaped shafts, and the 22 tooth pulley wheels with 3/8 round bore with a grub screw to keep in place. I have read on Joes CNC forum that some people have glued in the grub screws to stop them loosening, which has worked but I feel isn't an elegant or long term solution. Is anyone else having a problem like this? Are pulley wheels available with a d shaped 3/8 bore?