Try running sudo ~/RetroPie-Setup/retropie_setup.sh at the prompt or through SSH and then update all packages and see if that puts it back.

I don't get it. Which GUI do you mean, EmulationStation, RetroArch or what? And why should it be toggle able? If it's for EmulationStation, why not split the roms into the different systems?

@alexgtorres91 What makes you think options 3-7 really exist ? That's not an order number there, it's a hotkey to activate the option next to it.

There is another driver project for ILI9341 based SPI displays https://github.com/juj/fbcp-ili9341 that you can try, if you're still working on the project. That one is a full standalone solution that does not utilize modprobe or the kernel SPI driver. Installation instructions are at https://github.com/juj/fbcp-ili9341#building-and-running

@incunabula Touché

I think the good way id to create 2 core option files and launch the game with correct option file depending u want to launch in jap 60hz or use 60 hz or pal 50 hz. Is possible in gamelist to set the lauching command specifically for each game?

I found a way to reset controller settings finally and now I can setup my controller from scratch :D

See the documentation on the wiki https://github.com/RetroPie/RetroPie-Setup/wiki/lr-mame2003#mame-menu