Amiberry - deafult joystick (port 2) is not set when running games

[raspnoobie]

I am using amiberry with a keyboard encoder for my arcade joystick setup. I am able to run the games, but at every boot of Amiga games, the joystick is disabled, none of the buttons are working.
I have to go in the settings for every game (and every time I run a game, even if I played it before), and set the joystick in the controls dropdown because for some reasons, amiberry set nothing for joystick port 2 (the first port is the mouse).

I checked the folder where the config files are , and I see an emulators.cfg file and a amiberry folder. Inside that folder, I see a conf folder with the retroarch.cfg file; so the controls are set, but I can't find where amiberry save its own settings, so I don't end up with the joystick port 2 empty at every boot.

I would like to set it up so every time amiberry reboot, it will set my joystick instead of leaving the field blank. Is there a config file that I can modify for this purpose?