is it a problem with 
    Unattended-Upgrades::MinimalSteps "true"; 
?

** Attachment added: "output of $apt-config dump"
   
https://bugs.launchpad.net/ubuntu/+source/unattended-upgrades/+bug/1020680/+attachment/3230174/+files/apt-config_dump.txt

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https://bugs.launchpad.net/bugs/1020680

Title:
  unattended-upgrade removed kubuntu-desktop and related packages

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