I'm pretty new to mach3. I didn't have this problem in GRBL. I've been use fusion 360 for about 4 years. I'm having this issue where all my holes and cuts are off about the half half the diameter of my tool. All the hole dimensions are correct, so my axis steps are dialed in. Its the alignment to zero that is off. I'm zeroing the parts to the edges of my endmill. Example, I have a 6mm tool and my parts are out of alignment 3mm. Almost like its not adding 3mm or half the tool diameter.