Using your test script on Xenial I discovered that after the reboot I
needed to run 'sudo dpkg --configure -a' to finish the operations that
unattended-upgrades was doing.

Further testing has revealed that there seems to be something wrong with
Xenial while I'd been testing Yakkety.

When running your script on Yakkety I saw that unattended-upgrades-
shutdown.log was created and contained the following:

bdmurray@clean-yakkety-amd64:~$ cat 
/var/log/unattended-upgrades/unattended-upgrades-shutdown.log 
2017-05-24 14:56:03,095 WARNING - Unattended-upgrade in progress during 
shutdown, sleeping for 5s
Progress: 50.1385 % (linux-headers-4.8.0-52)
2017-05-24 14:56:08,110 INFO - All upgrades installed

While on Xenial unattended-upgrades-shutdown.log was an empty file and I
did not see anything on the shutdown screen about the shutdown being
paused.

Could you confirm that Yakkety deals better with a reboot while
unattended-upgrades is running? Thanks!

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https://bugs.launchpad.net/bugs/1690980

Title:
  No pop-up window to warn users that system should not reboot or
  shutdown while installing security updates

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