I was still getting this message on Debian sid w/kernel 2.6.22.6 and I
could hear my drive spin back up before the PC went completely off.
This was the fix
which was a small edit on the /etc/init.d/halt script. It worked on two
boxes.
http://www.linuxquestions.org/questions/debian-26/disk-might-not-be-spun-down-properly.-update-shutdown-utility-583307/
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