Jog distance increment and movement increment should be the same.
Usually difficulties such as you describe are caused by a disconnect in how the origin is specified in the file and how the zero is set relative to the stock, but that’s a greater adjustment than I’ve typically seen.
If you set Z origin at one point, then move away, then go back to zero you should return to where it was set, invariant of if the movement otherwise was greater or shorter than expected.
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Just commenting since I am surprised by such a large steps per mm factor. Back when I bothered to calibrate my axes, I rarely had to adjust outside of the 39.9 to 40.1 range.
I suggest troubleshooting this problem with the default GRBL values initially.
Any chance you might have positioned the probe on the corner of the stock and then probed Z only ?
I second the thought that there may be a translation/transposition/rounding error somewhere in the math to figure the steps, 42.8 is the largest value I have ever heard of to be entered in the $102 setting… Like @Julien, I would be wary of any value outside of the range of 40.20 to 39.80…
I would suggest a pair of pockets, one just deep enough to be certain it is cutting, the other some even metric measurement down, but not through the board.
Please write us at support@carbide3d.com and let us know about this — I think we should send you a new belt.
That math is not off, but any inaccuracy in measurement (or rounding) would likely be amplified by the tiny depth of cut being measured (similar to falsely extracting statistics using too small a sample size)…
Are you sure you don’t have a mechanical issue causing the shallow pockets? There should be no difference between a jog motion and any automatic motion.
If you want to calibrate using pocket depth, I would first face the stock so you’re starting from a perfect zero, and then be conservative with your depth of cut to rule out lost steps.
To figure out whether it’s lost steps or belt slipping/stretching during an actual cut, you could first check what distance the router mount travels when jogging 0.5" up or down, with a ruler next to it. A difference of 0.04" (like you got in that pocket cut) will be visible to the naked eye, but I would not be surprised that when jogging in the air you get very close to 0.5" actual travel, and the problem only occurs during cutting.