I was also annoyed by this beep and I managed to found a solution on another forum:
I have found the solution to this problem. Unfortunately - despite trying very hard on several calls - Toshiba Tech Service is not aware of it (as of January 2010), so I hope they pick up on this post.
The issue appears to be related to the "Realtek HD Sound Effect Manager" which is in Control Panel. Go to Start / Control Panel and open "Realtek HD Sound Effect Manger". At the top of the blue Realtek screen there are a number of tabs ("Sound Effect", "Mixer", "Audio I/O" etc). It won't immediately appear, but If you hit the button to scroll to the right (just to the right of the tabs), you will find another tab labeled "Power Management". (Note that this tab does not normally appear - you have to scroll to the right for it to become visible.) If you pick "Disable Power Management" and hit OK, it allows you to gain control over the volume of the low battery beep.
It was a relieve to found a solution!