Hi Peter,
Your GCode file runs just fine here.
After you have zeroed the Z axis at the spoil board level then at program run the first Z axis movement should be to +50.8mm above the spoil board. As you have said the first Z axis movement is downwards then, as you suspect, something in Mach3 is set wrong.
With the Z axis at a safe height zero the Z axis DRO and using the MDI screen type Z10 and press return. The Z axis should rise by 10mm and the Z axis DRO should show +10.0000. Does this happen ?
Tweakie.