"Factory reset" resets all custom settings to ensure there will be no conflicting settings due to user failure, unfortunately it is necessary to reconfigure what has been customized, but it is the most functional method for many problems: unfortunately it is faster/easier reconfigure than find out exactly what is conflicting.
@cristian-muñoz Okay, so you're telling, you have the joystick's mapping properly, but have you tried REDO this mapping after discovering that is not working in Kodi?
Also, you seted this control to player 1, but, have you tried to leave player 1 as automatic, and enter the kodi, to see if it works?
Another possibility: you claim that your joystick is a ps3 shawan, did you even try to change the driver in the recalbox.conf file? Enter the file "recalbox.conf" and search for "controllers.ps3.driver", there are 3 possible drivers, and 2 of them claim to work on shanwan joysticks, my file for example is like "controllers.ps3.driver = bluez", but can be changed to "controllers.ps3.driver = shanwan".