Comment 5 for bug 468589

If confirmed, this is an important issue.
I do not seem to be able to reproduce it here though, anything you did that might help recreating the problem?

What is the output of

cat /proc/cmdline
cat /var/run/sendsigs.omit

?

You might have to manually run the shutdown commands (/etc/rc6.d) in the right order from terminal until you find the problematic one (probably S40 or S60).