I have not had such problems with the vista machines we use here, however I would suggest that you contact support for the audio interface you use. My experience with vista doing odd things like loosing user settings have usually been traced to a driver or device issue.
My guess is there is obviously a vista bug related to this in there somewhere (an imperfect drivers shouldnt prevent vista from saving user settings), however it only seem to impact devices with imperfect drivers - which in our pro-audio world unfortunately seems to be quite regular.
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