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:
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: