When im using skype and have any program thats playing noise (youtube, itunes etc.) the sounds from those programs play over skype. This has happened on the same computer with both Mac and Windows (boot camp on macbook pro). I've looked in windows and where it shows my mic even with it muted it its picking up sound, which I would assume is from something running (again youtube, itunes, etc.). I'm using Turtle Beach X12's as my headset and using the mic on that and not the built in one.
it picking the sound mix system part as a input
need to change it some how with in the software ether sound mix
windows xp home i had same trouble, but i upgraded
sorry don't have a real asnwer, only recall what i look for when it happen
mostly game sound mix with the mic when i talk i had to mute or turn off other item so it didn't care over like windows playing music i turn that off or game i gone into the setting to turn off any fix/ music with in the game setting
i don't have this trouble windows 7
Control Panel>Hardware and Sound>Realtek HD Audio Manager (ofc if you have this driver), go at microphone and check Acoustic Echo Cancellation. This worked for me.