I have exactly the same problem on picodrive (but it happens with all emulators). If I config buttons on quick menu, controls, then save overrides, it doesn't reads on game launch (it says it does, but the controls config are back to default). If I config them on main menu, settings, input, when I go to configurations and I select save current configuration, it says:
failed saving config to "/recalbox/share/system/config
and it doesn't show the rest of the directory and file name.