Thanks, this happened when Unattended-Upgrade::InstallOnShutdown was
set.

I have uploaded a new u-u package to the ppa and updated the GitHub PR with the 
fix. Please give the package a try, it now works fine on my system.
I did not notice the issue because the download step was quick in my VM.

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

Title:
  unattended-upgrades does not block shutdown of system, as it is
  designed to

Status in OEM Priority Project:
  Triaged
Status in OEM Priority Project xenial series:
  New
Status in apt package in Ubuntu:
  New
Status in unattended-upgrades package in Ubuntu:
  Confirmed

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

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

  Steps:
  1. trigger unattended-upgrades
  2. reboot or shutdown system while installing packages

  Expected results: There is a pop-up window to warn users that system
  should not reboot or shutdown

  Actual results: There is no pop-up window to warn users

  Additional information:
  $ apt-cache policy unattended-upgrades
  unattended-upgrades:
    Installed: 0.90
    Candidate: 0.90ubuntu0.5
  $ lsb_release -rd
  Description:    Ubuntu 16.04 LTS

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