@bucweat I haven't had time to test it but I believe if you're using something like OctoPrint to feed G-code that G28 in the Start code disables bed leveling and has to be re enabled with M420 S1. I also follow it with a G29 O(that's Oh not zero!) to verify it was able to retrieve the bed mesh and if not run bed leveling again.
I asked this question on the CR-6 SE Facebook page but didn't really get a satisfying answer.
Also as far as I know you need to have an SD card in for the bed mesh to save to EEPROM even if you're using OctoPrint to supply G-code.