There are indeed three separate but possibly related problems
intertwined in this ticket:

1. PCSpeaker audio too loud.
I haven't noticed this problem myself, specifically. My laptop's PCSpeaker 
output is routed through my sound card anyway, possibly a BIOS function. 
Something interesting to note here, though: PCSpeaker output is *always* 
through my laptop speakers, whether I have headphones plugged in or not (HDA 
Intel). However, I do have a volume control setting for "Beep" on my mixer. It 
is currently muted (which has no effect on its output through my speakers), but 
unmuting it and turning the volume up results in it being output through my 
headphones as well.

2. Beeps at system shutdown.
I can confirm this one. The beeps in question are the alert beeps that normally 
happen when one issues a shutdown command in console. I have always heard the 
series of beeps whenever I issue a shutdown command within a terminal window, 
from TTY, or over SSH if I remotely shut down another computer. These are also 
distinct from the "system beep in lieu of alert sound" bug, as these beeps are 
of a much higher pitch. It's important to note that these beeps have *never* 
been triggered by a shutdown from desktop; only from a shell shutdown. It is 
only with Jaunty that the beeps are now accompanying a shutdown from desktop.

3. System beep in lieu of alert sound setting in Gnome Sound Preferences.
This is a separate bug from #2, and may or may not be related. I have had this 
bug for as long as I can remember (I joined the Linux community with Feisty). 
Gnome Desktop seems to have never honored my alert sound settings. Now, what is 
TRULY interesting here is that, although Gnome does not honor it, some non-GTK 
programs do - namely Second Life. Backspacing too far within the SL client 
causes your chosen alert sound to play. So, this is clearly a Gnome bug.

As for the Compiz situation: I do not understand why it has a system
beep setting. It seems to me that, if Compiz is going to be an official
part of Ubuntu, then it should be integrated far better than it is now.
This means forcing Compiz to honor all Gnome settings, rather than
forcing users to set window decorators, mouse pointers, and system beeps
in two different places.

-- 
Extremely loud and intrusive system beep with (some?) HD Audio devices
https://bugs.launchpad.net/bugs/331589
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