I noticed this on v5.24 and even after upgrading to v5.25.
when I am in any system. say nes/gb/genesis. these are some issues I noticed
1 - when I change options. even though I have auto config save Off when I make changes to options and exit without saving (for example to test a setting for that game only). when I leave the game and load another game the options stayed on. like if I have saved the setting to core override
2 - even when I save options for a specific game only the setting gets saved to the core so next games I load gets the setting
3- on gameboy emulator the setting won't stay saved. for example in options I changed the color scheme from gray to Super gameboy color and save the setting as core override. the next games I load will not have those saved settings.