Known, and intended behavior.
If you run an engraving, then some fills, and finally do a cutout, and 1 of the 5 items doesn’t cut all the way, you can turn off the other layers (or select just the object you want and enable Cut Selected Graphics) and LightBurn will re-run just that cut without affecting the origin, so the 2nd cut happens in the same place.
If you want the origin computed from only what you’re cutting, use ‘Cut Selected Graphics’ and ‘Use Selection Origin’, and select the stuff you want to cut.
LightBurn always shows the origin of the job as the green square on the page. If I have two objects, and have ‘Cut Selected’ enabled, this is my origin:
The origin moves here if I enable ‘Use Selection Origin’: