SNES should load the SNES specific config file found in the .config folder. In that config is a line to include the "all" config file for retroarch.

Look for this config and see if the include line is there and if it points to the correct "all" config. It sounds like when you load a ROM, the SNES emulator is not loading the SNES config file, so it creates one.

I'm not very knowledgeable with this, but you need to trace the config files. Retroarch also has a directory settings for configs. I believe it is set to "default" in the config. I know if you change this, it will cause problems.

I updated my firmware to: 2.68 and I couldn't get the thing to work properly. I rolled back to the 2.67 version and it all worked as before.

I didn't try starting the joypad in another mode other than select.

You could try linuxjoystickmapper. I have successfully mapped keyboard presses to my PS3 controller for the standalone PPSSPP emulator. For the life of me I can't use the built in mapper without getting some wonky response while in the UI menu, so I used linuxjoystickmapper and mapped all the default keyboard controls in PPSSPP to my controller. You can also map stick axes to keys, but I have had trouble with this. You might be more successful there.

Here is some more info should you decide to tinker with it: https://retropie.org.uk/forum/topic/2032/dosbox-mapping-mouse-to-ps3-analog-stick/17

I would consider it a last resort.

Whup, got this sorted, restart and bob's your uncle.

@dankcushions Because that's the latest version of SDL MAME Wii, which is where I will be playing games.
So I don't need the CHD files for a proper conversion - only if I intend to play the games which require it, right?

Coincidentally I have purchased and tested a cheap USB hub with 7 ports on my raspi1 today. Some ports doesn't work as expected, but I didn't have time to check it deeper.

Did you turn on the "Save config on exit" in RetroArch (config_save_on_exit = "true" in retroarch.cfg). I'm not sure but by your description it seems to be your problem (at least one of them).

BTW, maybe you like to know this tool: https://retropie.org.uk/forum/topic/1167/here-is-a-way-to-select-joystick-for-players-1-4-global-or-emu-specific

I appologize. I thought I had enabled the 360 controller. It wasnt. Once I did that it fixed the issue. So install the xbox 360 driver from retropie-setup supplementary menu

All working now. Thanks

Thank you for the super fast reply!

There must have been a bug in the dxx-rebirth code when the last binaries were built. I have updated them and save is now working again (as you found when building from latest release). Thanks for the feedback.

I understand. Thanks for taking the time to explain.

The script that meleu mentions is a great solution to have the GUI. My issue was apparently everything was writing below the #include line in the cfg files.

Once I moved my player joypad index lines above #include all was well.

Thanks for those that took a look, and super thanks to @meleu for the help & feedback.

@evilmurray If you do a software update won't it rebuild that directory?

@xxghostbusterxx

Read more about here:
https://retropie.org.uk/forum/topic/2582/can-my-usb-device-have-data-on-it-already/5

Keep track to link the right pathes but it should work without a problem.
Please do not change/edit es_config-file :)

... this sure is "important".