Comment 1 for bug 1981434

That's strange. Grub Customizer just runs the system command "grub-mkconfig" (or grub2-mkconfig) to detect operating systems. If you don't change something on Grub Customizers list config, it wont modify something on the detection scripts (/etc/grub.d). Look at this folder. Is there an extra folder named proxifiedScripts? If not, it must be another reason.

Btw.: There's a better way to add extra entries to the boot menu. Put it into /etc/grub.d/40_custom and then run update-grub or use the save button of grub customizer. Then your grub menu stays updatable.