No, it's not iTunes' fault.
I'm getting the same exact problems with BF2 now also! I can't hear the menu music, opening movies, or any weapon sounds.
I've determined it's not a driver or soundcard issue, as I've reinstalled the card with the original drivers and still had the problems, then, I updated to recent drivers and still had the problems. I've swept for spyware, viruses, and cleaned the registry. I'm at my wit's end.
I'm considering a reformat. Does this basically mean wiping all the data off my hard drive and reinstalling windows?