"DirectSound could not be initialized. If you are running any applications playing sound in the background, you should stop them before continuing."
Tell you what, why not try running the game on a dedicated X server?
I might be wrong, but that should pretty certainly make sure that there are no sound playing applications running at least on that X display's background... dunno if it's the active X display that counts, or all of them. Here
are pretty detailed instructions on setting FS2_Open to run on dedicated X server display... which is good practice anyway since when the FS2_Open jams and requires you to Ctrl+Backspace to kill the X, you'll only lose the FS2_Open, not all the applications you may or may not be running on the background, 'cause they are on the primary X display.
Don't know if this'll help with the sound problems or not, but I'd say it's worth trying at least.