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.

Hopefully this makes sense. I'm running an ethernet based smooth stepper from warp9. The parts just seem to be off half the diameter of the tool from zero.

Here is my fusion gcode. I'm just making some small inline test holes to check alignment

(MACH3-ALIGNMENT-HOLE-TEST)
(T14 D=6. CR=0. - ZMIN=-0.5 - FLAT END MILL)
G90 G94 G91.1 G40 G49 G17
G21
(WHEN USING FUSION 360 FOR PERSONAL USE, THE FEEDRATE OF)
(RAPID MOVES IS REDUCED TO MATCH THE FEEDRATE OF CUTTING)
(MOVES, WHICH CAN INCREASE MACHINING TIME. UNRESTRICTED RAPID)
(MOVES ARE AVAILABLE WITH A FUSION 360 SUBSCRIPTION.)
G28 G91 Z0.
G90

(CIRCULAR1)
T14 M6
S24000 M3
G17 G90 G94
G54
M8
G0 X6.45 Y12.5
G43 Z15. H14
G1 Z1.3 F150.
Z-0.1
X6.75
G3 X7. Y12.75 I0. J0.25
X6. I-0.5 J0.
X7. I0.5 J0.
X6.75 Y13. I-0.25 J0.
G1 X6.45
Z5.
Y12.5
Z1.2
Z-0.2
X6.75
G3 X7. Y12.75 I0. J0.25
X6. I-0.5 J0.
X7. I0.5 J0.
X6.75 Y13. I-0.25 J0.
G1 X6.45
Z5.
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Z1.1
Z-0.3
X6.75
G3 X7. Y12.75 I0. J0.25
X6. I-0.5 J0.
X7. I0.5 J0.
X6.75 Y13. I-0.25 J0.
G1 X6.45
Z5.
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Z1.
Z-0.4
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G3 X7. Y12.75 I0. J0.25
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X7. I0.5 J0.
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G1 X6.45
Z5.
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Z0.9
Z-0.5
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G3 X7. Y12.75 I0. J0.25
X6. I-0.5 J0.
X7. I0.5 J0.
X6.75 Y13. I-0.25 J0.
G1 X6.45
Z5.
X16.45 Y12.5
Z1.3
Z-0.1
X16.75
G3 X17. Y12.75 I0. J0.25
X16. I-0.5 J0.
X17. I0.5 J0.
X16.75 Y13. I-0.25 J0.
G1 X16.45
Z5.
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Z1.2
Z-0.2
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G3 X17. Y12.75 I0. J0.25
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X17. I0.5 J0.
X16.75 Y13. I-0.25 J0.
G1 X16.45
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G1 X16.45
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G1 X16.45
Z5.
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X17. I0.5 J0.
X16.75 Y13. I-0.25 J0.
G1 X16.45
Z5.
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Z1.3
Z-0.1
X26.75
G3 X27. Y12.75 I0. J0.25
X26. I-0.5 J0.
X27. I0.5 J0.
X26.75 Y13. I-0.25 J0.
G1 X26.45
Z5.
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Z1.2
Z-0.2
X26.75
G3 X27. Y12.75 I0. J0.25
X26. I-0.5 J0.
X27. I0.5 J0.
X26.75 Y13. I-0.25 J0.
G1 X26.45
Z5.
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Z1.1
Z-0.3
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G1 X26.45
Z5.
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G1 X26.45
Z5.
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Z0.9
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G3 X27. Y12.75 I0. J0.25
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X26.75 Y13. I-0.25 J0.
G1 X26.45
Z5.
X36.45 Y12.5
Z1.3
Z-0.1
X36.75
G3 X37. Y12.75 I0. J0.25
X36. I-0.5 J0.
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G1 X36.45
Z5.
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G1 X36.45
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G1 X36.45
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G1 X36.45
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G1 X36.45
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G1 X46.45
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X46.75 Y13. I-0.25 J0.
G1 X46.45
Z5.
X56.45 Y12.5
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G1 X56.45
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G1 X56.45
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G1 X56.45
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G1 X56.45
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X67. I0.5 J0.
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G1 X66.45
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G1 X66.45
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G1 X66.45
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G1 X66.45
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X67. I0.5 J0.
X66.75 Y13. I-0.25 J0.
G1 X66.45
Z15.

M9
M5
G28 G91 Z0.
G90
G28 G91 X0. Y0.
G90
M30

Its definetly the tool diameter zero offset. My endmill is 6mm. If I make the X and Y zero -3.0 it is perfectly aligned. I thought mach3 or fusion was supposed to compensate for this. You zero the edge of your tool and mach3 will compensate for tool diameter. Let me know if I'm wrong.

Suppose you have a test probe of 6mm dia which you mount in the spindle.  Then you touch this off an edge that you would like to be at the zero of the particular axis program coordinate, say the X axis.  When it is just touching the dro should be set to -3mm so the tool axis would pass through the edge if the spindle moves to X=0.