Very odd it cut fine when you ignored the etching–but was this on a different sheet?
Are you pinning the boards down? There are great hold down pins in the free designs Honeycomb bed holdown pins that are a MUST. Boards may look flat, but rarely truly are (tap on the board and you can tell if it’s tight to the crumb tray or not by the sound–more hollow = bit of a gap). And any non-flatness will not get a clean cut.
And magnets (but not the super strong rare earth ones) can help in the center of the board–just keep 1/2" or so from the laser path.
And a tip–before you move the sheet, try to wiggle your design to verify if it’s been cut thru yet or not. And without moving the material or the design in the GFUI, ignore the etching and the run another cut. (Lesson learned after losing jobs/material, too!).
Also many users always slow down their cut speed, since environmental conditions can affect the performance, too. I don’t always have to, but going down by about 10 always helps.