This too is a fix (used on Jaunty):
In the terminal, perform the following:
gksudo gedit /etc/modprobe.d/blacklist.conf
Then add the following at the bottom of the file:
blacklist pcspkr
Now restart your machine. Note that the beep will still sound when
shutting down. However, once restarted, try shutdown again. The
beep(ing) should now not occur.
--
Annoying beep on shutdown using "System -> Shut down..."
https://bugs.launchpad.net/bugs/290204
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