Using what you have created, click the ‘Optimization Settings’ button in the ‘Laser’ window, then tick the ‘Remove overlapping lines’ to ON (green) and then look at the resulting cut in the Preview. Moving the slider in that ‘Preview’ to see the cut process progression, are the overlapping lines being cut more than one time or are they removed?
You are using a different option to do the removal when selecting ‘Delete Duplicates’. LightBurn is aware that this duplicate shape deletion needs work as the current iteration requires the shapes to have a very close match to be removed. Work continues to enhance this feature.