I have no idea what could be the cause of this, I think that I also had this problem with TESIV Creation Kit as well. I understand that I can just mute my headphones, but often times when I'm using the Creation Kit I like to actually speak to people online or listen to music.
I'll also reiterate the problem since I know that this could probably sound confusing. The problem is that whenever I click on an item in one menu (for example clicking on a chair in the cell window) and then I switch to another window and click on something else (for example a door in the Object Window) it makes an extremely loud beeping sound, which I believe is one of the sounds from the Vista OS itself.
If anyone has any advice on what I could do to fix this, please let me know. It can get really irritating when every 2 seconds I I twitch and lose focus because of this dang noise.