As @thelmuth points out, measure lines marked on the surface, not cuts. Adjusting the kerf without accurate step sizes for both axes will only confuse the issue.
Measuring a cut square as you show also has issues. If the cut is not a clean perpendicular edge, you’re also measuring:
- Cut angle w.r.t. the top / bottom surfaces
- Edge irregularities
- Beam irregularities
- Axis angular misalignment
- Crud melted off the mask film
Don’t adjust the kerf to make the answer come out right. You must measure the kerf in that material, then set the offset accordingly:
Also, verify the head’s angular alignment to ensure it’s not cutting a diagonal on the Y-axis faces.
(I gotta start thinking & typing faster …)