@Skullborn For RetroArch emulators, there's hierarchy of configurations supported - see https://retropie.org.uk/docs/RetroArch-Configuration/#config-hierarchy. If you saved a content folder override for the configuration or used 'Save Configuration', I would expect that some configuration would be different, depending on your options set for each system. But - for each system - RetroArch has the same auto-configuration for joypads (created automatically after you configure your gamepad in EmulationStation), so I expect that if a gamepad is detected in one system, it should work in all systems. As for advmame, it doesn't obey any config hierarcy, so I would also expect the same configuration to apply for all systems.