I've had same issue on Vista 64 Ultimate / XFi for a few months as well, mainly on Skype. Usually, will start a call and I sound like a drowning dalek until I fiddle about with the sound and set mic as default as mentioned. Also have to do this within Skype as well and swap between Xfi Mike and Win default device on input. Trouble is it resets itself again (including mike gain / volume) if I drop the call and have to start all over!
Although saying that Skype has been a lot better since I moved it to a separate HD, for some bizarre reason.