Yes, I tried launching with Armory Crate and just using the shortcut LaunchBox creates. I've also tried using multiple emulators like NES and SNES and both do the same thing so I am not sure if its retroarch settings that have to be changed, but ill do my best to explain what is happening.
Regardless of how I launch the program this happens. When I launch the Launchbox program, everything seems to work fine. Buttons work, dpad works, etc. When I launch Bigbox, everything works also, like dpad, buttons to select game, etc. Once the game is up and running, and I get into game play, the A button seems to do two functions. When I press A button, the game will pause, when I hit it again the game unpauses and my character jumps. If I hit the B button I get a message that pops up saying "press again to exit". If I press B again it will take me back to bigbox menu where I can select a game. I've tried to make changes to the controller, but the buttons it says to press don't work as intended. For instance, the keybindings say to clear what one of the buttons does, Im to hit X to clear the binding, but when I hit X, it does a page down or up. Same with the Y button. So X and Y both act like page up and page down, so I cannot clear the keybind and assign a new one. Im sure it has something to do with the unit and compatibility, almost like its detecting the controller but also thinking its a keyboard, etc. I hope this clears up what is happening. Hope your getting better results with your new ROG Ally.
Thank you.