At the risk of sounding insane...
If there are sound problems only when you use gtk-recordmydesktop:

Run another ubuntu in virtualbox. DS emulator (in wine) can directly access the (virtual) soundcard there. Sound in virtualbox can run through pulseaudio. Then you can use gtk-recordmydesktop to record your (real) desktop.

I count a ridiculous amount of indirection there, but it should work .