retroarch won't save gamepad bindings

[DaFunkShun]

I have no idea what I am doing wrong and need help please!

I setup my hotkey bindings in the configuration menu of retroarch without having a core loaded (Settings - > Input -> Hotkeys)
and when done save them in the main menu (Main Menu -> Configuration File -> Save Current Configuration).
This worked perfectly.

I then loaded a core (Flycast) and all my settings are gone, retroarch loading retroarchcustom.cfg instead of retroarch.cfg
I redid all my key bindings and saved them as current configuration under the same name (retroarchcustom.cfg) but my settings are not saved and I have to rebind my hotkeys every time I start a game.

I then edited the retroarchcustom.cfg manually and added the hotkeys but found out that retroarch just recreates a 'default' retroarchcustom.cfg every time it loads Flycast.

What am I missing ?