Have this too, sometimes. The music plays for a while, then it fades away and i only hear FX. And i don't know if it's related, but on some occasions, some FX sounds are muted, mostly battle sounds (like spells, attack, etc), and i can only hear music, the wind and the sound made when i command my demigod (or minion) to attack or move.
These sound bugs seem to appear when i sit for too long in the lobby or at map loading screen, or after some alt-tab. Really weird as i can't pin point the cause and recreate it.
Vista x64 with X-FI Music sound card (latest drivers, sound set in-game to high with reverb).