I'm having a problem similar to this with SegaCD games. They're structured like this:
 
	Game(NTSC)(US)\
 
	     Game(NTSC)(US)[!].cue
 
	     Game(NTSC)(US)(Track 01 of 12)[!].iso
 
	     Game(NTSC)(US)(Track 02 of 12)[!].wav
 
	     etc
 
	If I tell it not to merge duplicates, it creates an entry for every file. If I tell it to merge duplicates, it correctly creates one entry, but if I Play it, it tries to launch a random WAV file in RetroArch. If I pick a version and select the cue file, it works.