Sorry for the late reply. I just realized what is wrong. In the passes tab of your cut operation it is worth setting up a lead in and lead out. A good starting point for both lead in and lead out is an arc radius of 1mm (0.04") and a line length at least equal to your cut depth. Set the angle to 45 degrees for lead in and 0 for lead out.
The lead in/out addresses that issue nicely, thanks.
