the problem is when engraving, when cutting everything is absolutely fine.
PWM signal on and off tested. The result is still the same.
Speed reduction to 25mm / s the same as for mode. The result is still the same.
Axis calibration. The result is still the same.
From what I can see in the pictures, the engraved part came out like a skewed oval, but the source file has it as a centered perfect circle. I think it has to do with rising verses falling edge settings on the controller.
This explains it well, as well as documenting the solution: