Upon closer inspection, my problem seems to be this:
Loading mod 'alternate_music'...
DLL loaded at 0x65A80000
Mod has settings file!
Setting name: 'playlist'
Setting value: 'MF'
Setting name: 'preload_songs'
Setting value: 'False'
Setting name: 'predecode_songs'
Setting value: 'False'
Setting name: 'fade_in_previous_song'
Setting value: 'False'
Setting name: 'pause_when_focus_lost'
Setting value: 'true'
Setting name: 'volume'
Setting value: '100'
Mod's debug output:
playlist.txt: song 'Pxtone/MM3Top.ptcop'
End of mod's debug output
Done loading mod
Dispite the fact that my playlist looks like this:
Pxtone/MM3Title.ptcop
Pxtone/MM3Top.ptcop,
Pxtone/MM9S.ptcop,
Pxtone/MM10Sol.ptcop,
Pxtone/NG1-42.ptcop,
Pxtone/NG2-22.ptcop,
Pxtone/Ng3-42.ptcop
Pxtone/P4Boss.ptcop
Pxtone/P5Boss.ptcop
Pxtone/CW.ptcop
Pxtone/GE007C.ptcop
Pxtone/GGDiz.ptcop
Pxtone/MM3Title.ptcop
Wow, simply deleting the playlist file and replacing it with an identical file fixed it. Thanks for the help anyways.
And now the sisters are bugged and won't deal any damage, great.