I was having issues with all my non-root filesystems never being unmounted correctly on shutdown/reboot, after much investigating the solution was incredibly simple:
http://ubuntuforums.org/showthread.php?t=1783047
It seems having all main shutdown (or reboot) script at the same run sequence number as many other scripts means that these are executed before these other critical scripts have completed - including unmounting these filesystems!
I know this affects 10.04 systems as a new test 10.04.3 install had the sequence set the same instead of last. It is ok in the 10.10, 11.04 & 11.10 beta systems that I have.
It seems to have been reported here: https://bugs.launchpad.net/ubuntu/+s...it/+bug/739007
If you have issues with your root filesystem not being unmounted cleanly then you may want to check this bug:
https://bugs.launchpad.net/ubuntu/+s...it/+bug/616287
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