hi tafazzi!
this is really weird. What controller are you using? Perhaps you could try to remove the es_input.cfg file from the .emulationstation directory? After the deletion of this file, reboot your raspberry and EmulationStation should bring up the input configuration menu where you’ll be asked to press various buttons on your controller.
in order to remove the file, locate the “.emulationstation” folder located in the home directory (/home/pi/). The es_input.cfg file should be there. on the command line you could type the following:
$ rm /home/pi/.emulationstation/es_input.cfg
$ sudo reboot
hope this helps.
cheers,