I had big time troubles with this for a while, but I came up with a possible solution. 
Find your 'title' sound file and change it to an .ogg. Go into your system file and adjust it to this .ogg file.
If yours works like mine does, you will go into MUGEN and your title music will skip like crazy at first.  Pick arcade, training, or survival and then go back to the title screen. For some crazy reason, not only does this make my title music completely fixed, it also fixes all of my in-game music. 
Because this really doesn't seem to make sense, maybe this won't work for anybody else, but it works wonders on mine. Give it a try!