My first guess if you have not fully setup Retroarch in Launchbox, more specifically the command line parameters in the associated platforms list for it. Launchbox does auto fill with a default list when the emulator in Launchbox is called Retroarch but if it is named something else it may not. The auto populated list though may not be what you are using so you will either need to adjust the command line or add a line if required.
Take a look at this video I did a little while ago, it covers the smaller details with Retroarch in Launchbox.