Still having the same issue with the latest 13.25 update so I fixed it manually, here's how:
Open [Launchbox Install Folder]\Data\ImputBindings.xml with a text editor
Insert the following lines and fill in the controller numbers you want to use
<InputBinding>
<InputAction>BigBoxExitGame</InputAction>
<ControllerHoldBinding>Button7</ControllerHoldBinding>
<ControllerBinding>Button8</ControllerBinding>
</InputBinding>
If you need to find out what the button numbers are then under windows go to "Set up USB Game Controllers", pick your controller and click on properties. It will bring up a screen with all available buttons with their numbers, when you press the buttons on your controller the appropriate number will light up.
Hope it helps!