This can be really annoying.
If the game can't detect
every piece of hardware used in a control config, it won't load it and it won't tell you it hasn't loaded it - you have to try to start using it. It won't even show you the option to select the config, even though the .binds file is still there. On my control setup, this can be particularly irritating as sometimes I don't find out until I try to launch the ship and my joystick isn't working.
There is a bindingloadingerrors.log file in the same directory as the binds file which will show you the USB ID of the device that wasn't initialised. This can help with troubleshooting, especially in combination with
USBDeview, which will show you the USB ID of the device next to a human readable device name.