Debian-built versions of visualboyadvance or self-built versions from current cvs (post 1.7.2, pre 1.8.0) produce garbled sound.
Given the history of cast wankery in the sound source to make it compile, are you sure the code is 64-bit clean? Just a hunch.
In general there is a sort of .. low pitch triangle wave (not sure if that's exactly correct) sound that overlays the music as if it is a misfired synth line. Although various aspects of the music are wrong to an extent.
I should really make a recording. I'll see what I can do.
what game?