Retroarch: input config doesn't work anymore after reboot

Hi everyone.
I’ve got a weird issue. I’ve got several games using LibRetro (Mame, Genesis, PSX games…). I can open RetroArch menu (F1) and config my X360 Wireless Controller without any issue.
But… Each time i reboot or shutdown my PC, next time my controller doesn’t work neither my keyboard, so i can’t even make RetroArch menu show up.
All i have to do is delete /home/username/.local/share/Lutris/runners/Retroarch/retroarch.cfg file, run again any game, so it recreates the file from beginning, and then i can use my keyboard and config again my controller.

Does anyone know what could be the issue?
Thanks in advance…