I couldn't find "E:\My Music\Pink-Floyd-The-Wall,The-Film-(Soundtrack)-1982\09 - Mother.mp3" listed anywhere in main.dat
I found:
E:\My Music\CD's I Own\Pink Floyd - The Wall\06 - Mother.mp3
E:\My Music\Pink.Floyd.-.[Is.There.Anybody.Out.There,.The.Wall(Live)](MP3)\Is There Anybody Out There, The Wall Live 1980-81 - Cd 1\Pink Floyd - (07)Mother.mp3
And I found "E:\My Music\CD's I Own\Rammstein_-_Mutter\03-Sonne_Rammstein.mp3" listed once.
Are you sure that these media library entries are exact duplicates of the exact same files with the exact same path & filename?
The reindexer will only remove exact duplicates. It won't remove anything if the path\filename is different.
Have you tried doing: Library button > Remove missing files...?
[Edit]
Okay, I loaded your main.dat/main.idx into a clean install,
and sure enough, I can see the duplicate entries.
Weird!
Thanks :-)
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