Okay... if u didn't have ur problem solved by the link posted, I have another solution. I recently had a problem with mp3s, coincidentally, and wound up having to switch to .ogg. Now everything works perfectly. Here's a quick overview:
*I copied a music configuration file from the mugen.cfg file of a program that had perfect music playback (don't worry, ill post it in a spoiler at the bottom of the page)
*I also took the plugins from the program (IF U WANT THEM, YOU'LL HAVE TO TELL ME CUZ IM NOT GONNA POST THEM ON ESNIPS FOR NO REASON)
*I downloaded a free .ogg converter from www.download.com
After all that, your music should work fine. Also, check ur speaker acceleration:
*Open control panel
*Sounds and Devices
*Speaker settings- Advanced
*Performance- Hardware acceleration (most say slide it all the way left, but for some reason that made it worse for me). Toy with this after u did evrything else
Lastly, don't forget to change ur music extensions in ur system.def
Hope it helps 
almost forgot the music config.
Spoiler, click to toggle visibilty
;-------------------------------------------------------
; Sound configuration (Windows)
; Note: WavVolume and MidiVolume here are not the same
; as the ones in [Options], but they all affect the volume.
[Sound Win]
;Set the following to 1 to enable sound effects and music.
;Set to 0 to disable.
Sound =1
;Set the following to 1 to enable stereo effects in-game
;Set to 0 to disable.
StereoEffects =1
;This is the width of the sound panning field. If you
;Increase this number, the stereo effects will sound
;closer to the middle. Set to a smaller number to get
;more stereo separation on sound effects.
;Only valid if StereoEffects is set to 1.
PanningWidth =240
;Set the following to 1 to reverse left and right channels
;on your sound card.
ReverseStereo =0
;Wave device to use. Choose from:
; NONE - No wave device
; AUTO - Autodetect
; DX? - DirectSound: replace ? with a the device number (from 0 to 9)
; DXA? - DirectSound with Allegro mixer: replace ? with a the device number (from 0 to 9)
; WAVEOUTA- High-quality wave-out
; WAVEOUTB- Low-quality wave-out
WavDevice =AUTO
;Voice Channels to use. Values are from 1 to 16.
;If sound quality is poor, try setting a smaller number, such as 8 or 4.
WavChannels =14
;Maximum number of voices used for MODs. This number reduces the
;number of available WavChannels. ModVoices must be less than
;WavChannels. If equal, then MODs will get all the available
;channels and therefore no sound effects will play.
ModVoices =6
;Midi device to use. Choose from:
; NONE - No midi device
; AUTO - Autodetect
; MAPPER - MIDI Mapper
; MID? - MIDI Device: replace ? with a the device number (from 0 to 9)
; DIGMID - Allegro's Digimid driver
MidiDevice =AUTO
;This is the master volume for all wav sounds (affects mp3 volume).
;Valid values are from from 0 to 255.
MasterWavVolume =100
;Set the volume of wav, midi, mods and CD audio.
;Note: WavVolume does not affect mp3 or mod volume.
;Valid values are from from 0 to 255.
;For CDAVolume only, using -1 will leave the volume unchanged.
WavVolume =100
MidiVolume =192
MP3Volume =255;This affects all Winamp-compatible plugins as well
ModVolume =80
CDAVolume =-1
;Set the following to 1 to enable and 0 to disable MIDI, MP3, MOD and CD
;playback.
PlayMIDI =1
PlayMP3 =1;This affects all Winamp-compatible plugins as well
PlayMOD =1
PlayCDA =1
;Set the drive letter of your CD-ROM (if you have more than one
;drive). eg, To use drive E, put the following:
; CDADevice = E:\
;Leave blank to use your default CD-ROM drive.
CDADevice =
;Set the following to 1 to pause BGM playback when switching
;away from the MUGEN window.
PauseBGMOnDefocus =1
;List Winamp-compatible plugins here.
;Specify the filename of the plugin and the list of file types to
;use the plugin for. One plugin per line.
;Example: plugin = plugins/my_plugin.dll, mp3, mp2, mpg
;
;If music is not looping with a particular plugin, you can try an
;optional first argument looptype=1 (seek to zero; may stutter)
;or looptype=2 (reload plugin; slow).
;Example: plugin = looptype=1,
plugins/my_plugin.dll, mp3, mp2, mpg
plugin =looptype=2, plugins/in_mp3.dll, mp3, mp2, mpg
plugin = plugins/in_vorbis.dll, ogg
;-------------------------------------------------------
; Sound configuration
; Note: WavVolume and MidiVolume here are not the same
; as the ones in [Options], but they all affect the volume.
[Sound Linux]
;Set the following to 1 to enable sound effects and music.
;Set to 0 to disable.
Sound = 1
;Set the following to 1 to enable stereo effects in-game
;Set to 0 to disable.
StereoEffects = 1
;This is the width of the sound panning field. If you
;Increase this number, the stereo effects will sound
;closer to the middle. Set to a smaller number to get
;more stereo separation on sound effects.
;Only valid if StereoEffects is set to 1.
PanningWidth = 240
;Set the following to 1 to reverse left and right channels
;on your sound card.
ReverseStereo = 0
;Wave device to use. Choose from:
; NONE - No wave device
; AUTO - Autodetect
; OSS - Open Sound System
; ESD - Enlightened Sound Daemon
; ALSA - ALSA sound driver
WavDevice = Auto
;Voice Channels to use. Values are from 1 to 16.
;If sound quality is poor, try setting a smaller number, such as 8 or 4.
WavChannels = 12
;Maximum number of voices used for MODs. This number reduces the
;number of available WavChannels. ModVoices must be less than
;WavChannels. If equal, then MODs will get all the available
;channels and therefore no sound effects will play.
ModVoices = 6
;Midi device to use. Choose from:
; NONE - No midi device
; AUTO - Autodetect
; OSS - Open Sound System
; ALSA - ALSA sound driver
; DIGMID - Allegro's Digimid driver
MidiDevice = Auto
;This is the master volume for all wav sounds (affects mp3 volume).
;Valid values are from from 0 to 255.
MasterWavVolume = 255
;Set the volume of wav, midi, mods and CD audio.
;Note: WavVolume does not affect mp3 or mod volume.
;Valid values are from from 0 to 255.
;For CDAVolume only, using -1 will leave the volume unchanged.
WavVolume = 128
MidiVolume = 128
MP3Volume = 135
ModVolume = 80
CDAVolume = -1
;Set the following to 1 to enable and 0 to disable MIDI, MP3, MOD and CD
;playback.
PlayMIDI = 1
PlayMP3 = 1
PlayMOD = 1
PlayCDA = 1
;Set the drive letter of your CD-ROM (if you have more than one
;drive). eg, To use drive E, put the following:
; CDADevice = E:\
;Leave blank to use your default CD-ROM drive.
CDADevice =