sjhurst: I have the same mod version (and running Windows7). On my system, this issue occurs when clicking on the desktop (the music stops), or opening another program, and then clicking on the game window (at this point, the music starts back up, but sounds crackly).
I've found that Hitting F4 to exit windowed mode and F4 again to re-enter windowed mode, fixed the sound/music. I didn't even have to close the game. It's not a permanent fix, since everytime you leave and return to the game window, you have to do this sound fix. But it's easy enough though, since it only takes a few seconds (hit F4, F4) each occurance.
After messing with my options for an hour, I got it to a point where I have a comfortable windowed resolution where the F trick that sjhurst mentioned works (thanks!).
The problem I was having is that I couldn't get the F4 trick to work when I was using the 32-bit MMX (stretchable) color mode. I really liked the stretchable mode because I could resize the window to fit my screen better, but it doesn't seem to work with the F4 trick.
The solution for me was to use the 32-bit GDI color mode (non stretchable) and find a resolution that was big enough to use enough of my screen space, but not too large that it would not allow me to scroll the window by moving my cursor to the sides of the window.
For my 22-inch monitor, running at 1920x1080 resolution, I set the game resolution to 1600x900 which works pretty well for me. A screen shot of what it looks like can be seen here:
http://imgur.com/vRICaDU