Ok, you have a couple of issues here, the main one and the cause of these troubles in the first place is you imported files to Launchbox that you shouldnt of. As you have noted the file that is loaded to the emulator is the .gdi file, but you imported everything, you only need to import the .gdi file. So i would just delete the game and drag and drop the .gdi file only to Launchbox to import it.
As for it picking the wrong file by default, that wont be a issue if you import the correct files, but you can right click the game, go to edit, go to additional app, this will list the files you imported, click on the gdi one and click the make default button to have that the file launched.