Fusion
In addition to @LibertyMachine's post, I would add a couple questions:
1) Does the machine have limit switches? If not, how is it homed?
2) How are you setting your work offset on the machine itself?
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It sounds to me that you need to establish what is called "Tool Height Offsets". Mach 3 does support them, and while it is possible to run the machine without them, it can make things easier.
What a Tool Height (Length) Offset does is this:
Your program XYZ values are relative to a position you define in your Fusion Setup. This is important to keep in mind when you get to the machine and actually set the job up. X and Y need to be defined in the machine, so it knows where the material is located. This is typically called the Work Offset, or G54, G55 etc. For the Z value, this is often controlled by your Tool Length Offset. This is the distance that the spindle needs to travel from it's home position until the tool is touching the part, or the touch off block, or some predetermined point (I use a 1" chinese gage block to touch off my tools so I don't mark the part). This value would then be entered into this section here:
