I was getting this problem in 12.10 and I continued to get it after an
upgrade to 13.04.

Today in 13.04 I edited /etc/rc6.d/S90reboot to run sh and examined the
situation. (If I simply ran sh, I got no output, just like other
messages in that script aren't displayed. I ended up using "sh <
/dev/console > /dev/console 2>&1" and then repeatedly trying to run
commands because something was taking some of the input. You may want to
just add a lsof command redirecting to a file followed by a sync
instead.)

I ran lsof and got the attached output. Please ignore references to /o because 
that is the lsof output file. The output shows one file being written: 
/var/log/upstart/ureadahead-other.log by init. I don't need that service, so I 
solved the problem by disabling it:
sudo sh -c "echo 'manual' > /etc/init/ureadahead-other.override"

I guess the proper solution would be to add a stop condition to 
/etc/init/ureadahead-other.conf, for example:
stop on runlevel [06]

** Attachment added: "lsof.reboot.txt"
   
https://bugs.launchpad.net/ubuntu/+source/sysvinit/+bug/1064185/+attachment/3665015/+files/lsof.reboot.txt

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https://bugs.launchpad.net/bugs/1064185

Title:
  root partition not unmounting cleanly on reboot

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