It is definitely coming from the motherbaord and not out of the sound system. I have tried with the headset in, muting the sound, etc, it makes no difference to the sound level.
I think it beeps once when powering up, but is sounds like the standard boot-up beep.
I have looked in the Task Manager to try and figure out if there is a particular program/process running/using resource but it was not obvious. The vast majority of teh time I am just using microsoft Office suite.