Ok, interesting; so it's the --hard-disk-standby code that causes  your
disk to get restarted ... this means the following is likely:

 - drive is downed by /sbin/reboot
 - drive comes back up for some reason
 - drive is downed by kernel

Can you do the following for me:

 - switch to a console (alt-f1 or ctrl-alt-f1 within X)
 - run (as root) "telinit 1"

That should (after a few seconds, you'll need to wait) give you a root,
single-user shell.

 - run "echo 8 > /proc/sys/kernel/printk"
 - run "echo 1 > /proc/sys/vm/block_dump"

You'll now start getting messages whenever the kernel needs the disk.
(Test that with "touch /foo" or something if you like).

 - run "halt --debug --force --hard-disk-standby"

Note where your disk spins down, and up, and see if you see can see what
is causing the disk to be brought up again.

You should see something like:

  PROCESS(PID): WRITE block NNN on YYY

or maybe

  PROCESS(PID): dirtied inote NNN (FILENAME) on YYY

If you could copy those, that'd be useful (don't worry about the
timestamps)

-- 
Hard disk stops and restarts on shut down
https://launchpad.net/bugs/61763

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