It has happened to me in several games of amiga that creates two or three m3u files but they are few it is not a problem I have corrected it by hand
I think it's a problem with how the files are named.
Indiana Jones and the Fate of Atlantis - The Graphic Adventure_Disk9
Indiana Jones and the Fate of Atlantis - The Graphic Adventure_Disk10
a suggestion, it would be great if it also created m3u files from the simple files