This is still broken in Ubuntu 9.10.  I don't know what the root cause
was going back to 6.06 but here is what is going on in 9.10.  I can't
believe the importance is low, this probably affects every single server
installation.  I am tempted to file a new bug as this one is so old and
it looks like Ubuntu just doesn't care.

ntpdate is supposed to be automatically run after a network connection is 
available, started by the script:
/etc/network/if-up.d/ntpdate

If /usr/ is on a separate partition from /, as most servers would do,
the network can be up before non-root partitions are mounted.

To deal with that, there is this section:
# This is for the case that /usr will be mounted later.
if [ -r /lib/udev/hotplug.functions ]; then
        . /lib/udev/hotplug.functions
        wait_for_file /usr/sbin/ntpdate-debian
fi

however /lib/udev/hotplug.functions does not exist, so it doesn't wait
for /usr/ to be mounted, and the time never gets synced because
/usr/sbin/ntpdate-debian is on the /usr/ partition which is not mounted
yet.

hotplug.functions does not exist in any Ubuntu package as far as I can
tell, but it is in the udev package of Debian Lenny.

I found some other bugs referencing /lib/udev/hotplug.functions so there
is probably a bigger problem than just broken ntpdate functionality.

In trying to make the boot process a few seconds faster and win over new
linux users, Ubuntu has broken all sorts of functionality that the core
linux audience depends on.

-- 
No NTP-Sync during bootup if /usr on different filesystem
https://bugs.launchpad.net/bugs/44166
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