What is you system/soundcard?
One of my computers has an onboard sound chip (Realcrap ... I mean Realtek) that exhibits this same behavior. Needles to say, it's not used for anything other than games and media players. Even then, I use it's optical S/PDIF output to feed the signal to an 828mkII.
Muting the Mic and CD on Playback controls as well as having their levels turned all the way down (and making sure the Mic boost is off) on Recording controls has helped.
That and using PS2 ports for the mouse and keyboard (If I remember correctly, the Realcrap was sharing an IRQ with USB).
Not sure if any of this pertains to your system or not .... but that's been my experience with the issue you describe.
HTH
-Ken