Hey Dan,
I cannot see that the g-code is the cause of your issue. Unfortunately I have no experience with the new Elite machines, their stepper motors nor the Masso G3 Touch controller. On the Standard Series with the open-loop steppers and the buildbotics.com-derived Onefinity controller, I would point you to the documents already linked above:
It would do no harm to have a look at them though to see what different causes such issues can have. But with no experience with the Elite machines, I can only refer you to Elite users who have experience with that issues or to support@onefinitycnc.com.
Note that when you probe Z from the top of the workpiece, the g-code takes this as the workpiece zero, however if you probe Z again but on a point that has already been milled away, it will take the new height as the workpiece zero height and will mill subsequently from this lower position.