I found these threads about it, as well.
This link speaks of it being in the EPROM, about which dictionary.com says:
QUOTE
a memory chip whose contents can be erased by a mechanism using ultraviolet light and reprogrammed for other purposes.
Another link.
Your only choice is to mute the chime completely, and I've used AppleScripts forever to do that. In OS X I use these instead of the usual restart and shut down commands in the menu bar. They mute the volume so the computer starts without the chime the next time.
tell application "System Events"
set volume 0
restart
end tell
tell application "System Events"
set volume 0
shut down
end tell
If you want to try them, start AppleScript then paste each one into a separate blank and save it as an application in the drop-down menu next to File Format under the window. Then uncheck everything. But you can leave Hide Extension checked, if you want.
You can save them in the Applications folder, and from there drag them into the dock.
Paste the following script into another AppleScript blank and save it the same way, and drop it into the Applications folder, as well.
tell application "System Events"
set volume 3
end tell
Or you can set it to 1 or 2 or 4 or 5, etc. — whatever number best matches the setting of your speakers' volume control.
Then go to Accounts in the preferences, and add this script to the log-in items, so it runs automatically every time the computer starts. The volume won't turn up until after the now-muted chime has triggered.