Im by no way or means an expert at RA or launchbox but just wanted to share my experience as it sounds like the same issue I had pulling my hair out for a longtime on this where loaded a game saved overrides etc exited the game and the controls were back to what they were when loaded again, ended up being very simple thing that I missed. Launchbox was simply loading up an older config via the extra command line parameters and not the one that was saved recently in RA, the command line is no longer required you can just select the core you are using and should work, I deleted the command line parameter found in the edit emulator window and hey presto it worked after a lot of headaches ? hope this helps