Thanks for the suggestion, but my individual emulator config files basically are empty apart from a few joystick overrides I have put in them to switch some keys depending on the emulator.
However, I have also thought that perhaps the 3 shaders which are setup by default may be stored somewhere, I just don’t know where and the logical place where the settings would be in the config/all/retroarch.cfg does not contain the settings.
When you apply shaders, the RGUI shader settings are saved to a temporary file (either rgui.cgp or rgui.glslp) and loaded. The file persists after RetroArch exits. The file is saved to video_shader_dir directory in config. If you always want to load the RGUI preset on bootup, you can set video_shader option to this file.
Further it says:
While you are changing settings in runtime, they are not saved to disk afterwards on PC by default. If you want RetroArch to automatically write back the config, either set config_save_on_exit = true in config, or enable this under Settings -> Config Save On Exit from within RGUI.
I will see if this fixes my problem and report back.
Time for my mea culpa. After fiddling around and not making it work, I rechecked the individual emulator files and found that the SNES and Megadrive one indeed to have override settings. After turning these off my shader settings are indeed sticking.