After dorking around with retroarch and rocketlaunch. I finally just used the built-in launcher in launchbox. Not only did it work. But I was able to add pre post applications so that I could reprogram my ultrastick for 4way or 8way or flightstick mode on the fly. I had some trouble with Daphne but at the end of the day I just created a batch file with the commandline settings the DaphneLauncher used and pointed launchbox at it. This worked flawlessly and I think it even pop's up faster than either of those two launchers.
It seems I can also add custom commandline options per game as well as global settings in the emulator settings of launchbox. I have yet to figure out why I needed them in the first place? I'm sure it will works just as well for the other platforms also.