I’m not sure what exactly causes this problem, but one of my computers running Kubuntu 9.10 has had this problem involving a long system beep during shutdown. Blacklisting the pc speaker didn’t work, nor did relentless searching for answers, until a post on Ubuntu forums finally answered my question.
The fix involves disabling the splash screen:
Edit /etc/default/grub
$ sudo nano /etc/default/grub
Change
GRUB_CMDLINE_LINUX_DEFAULT="quiet splash"
to
GRUB_CMDLINE_LINUX_DEFAULT="quiet"
Update Grub:
$ sudo update-grub
..and reboot!
On the first reboot, you may still hear the beep. Reboot twice before you assume it doesn’t work!
Credit: dimoftheyard