Yeah, just watched the video posted, in this specific issue you are launching a Turbografx-16 CD game, but when you go to the associated platform tab for Retroarch you only have a entry for Turbografx-16. You need to add another associated platform for the CD version, they are different systems in your Launchbox sidebar, so need separate entry's in the associated platform tab also.
EDIT.
This is why adding the commandline to the games works, Launchbox doesnt know which core to use for that platform as it is not in the associated platform list. Obviously adding it per game tells Launchbox which core to use, so it loads correctly then.