Totally muting the audio could potentially be a side-effect of using the DSP ROMs that Dolphin comes with. You need to dump the DSP ROMs from a GC or Wii. The DSP ROMs Dolphin has don't work with the GBA <-> GCN connectivity. Real DSP ROMs from a console is the only way to ensure proper audio emulation for these kinds of games at this time.
At the very least, try using Real DSP ROMs to see if it fixes the problem. If not, then we know it's gotta be something else.
At the very least, try using Real DSP ROMs to see if it fixes the problem. If not, then we know it's gotta be something else.