You have an issue with your machine slipping or losing steps. There is no such grouping behavior in LightBurn. If you “save GCode” between the two different files (one grouped, one not) they are probably just run in a slightly different order, and that difference in the order might be helping your machine not skip.
Run your saved GCode from LightBurn in an online GCode simulator to prove it.
Save the GCode using the two different options you’re talking about. Open each file in a text editor, then copy and paste the text into an online simulator if you don’t believe me: https://nraynaud.github.io/webgcode/
They’re the same. The difference is in the order your machine will run them, and a different order can sometimes be the difference between skipping and not skipping if your settings are too aggressive for the machine, or the machine is loose.