I’m betting it’s XY torque in your z axis from radial load. That’s what is happening in mine. I get the same .5mm undercut in dimensions as you when cutting anything harder than ultralight MDF. Even with very light cuts and slowed right down. Sharp tools and powerful spindle. And I can twist the Z assembly just about that much with my hand measuring with a test indicator. Little more play in the X than the Y. The play is all in how the spindle plate is attached to the carriage through the makerslide. Not slop – the wheels are tight. I see it as the give between the softer Delrin wheels and the V rail + torque on the Makerslide. It’s a garbage design. The spindle axis sits way too far out from the carriage and give so much mechanical advantage to radial leverage. I’m in the middle of replacing the whole slide with a linear bearing setup that halves the distance from the carriage, having stiffened up the Y axis with 3/8” plate to get rid of Z and X deflection happening there.
My step calibration is spot on over 700mm with nominally zero backlash. No steps being lost or belt skips. Belts are tensioned to exactly 5.1 lbs @ 1”.
Try this:
Instead of a profile cut, mock up some test dimensions and just plunge some scratch points with an engraving/vcarve bit. No XY cuts, just Z.
Or hot glue a fine line marker to your machine and draw some measurements. Something that excludes the drag on XY.
If the measurements between points are good (they were for me), it’s most likely twist in your Z assembly when under load. I’m betting your machine returns to exactly the work origin after a job too, right? If so, you aren’t losing steps.
And if all the above tests confirm this, throw away the Z assembly that’s on there and buy or make a proper one that’s coupled right to the gantry carriage.
I agree that for for $1500USD it’s disappointing that you have to put so much work into fixing deficiencies. I don’t expect it to be what a $5K or $10K machine would be, but for the same component cost as what comes with the Z assembly out of the box, it could be a much better design. Had I known, I would have bought it without the stock Z slide and simply bought a readymade bolt-on proper slide.