Jarno Suni,

That possible cause seems irrelevant to Unattended-Upgrades. Any
package installed by any front-end to apt will be upgraded. U-U doesn't
know what packages are installed, nor care. U-U simply tells aptdaemon
to upgrade packages from the repositories authorized by the user. U-U
does not duplicate nor replace Software Updater, and both can safely be
used.

Try running 'apt autoremove' (16.04) or 'apt-get autoremove'
(12.04/14.04).

If those kernels are not removed, then your problem is the apt-marking, 
not U-U. There are several ways to prevent automatically marking kernel
packages as 'auto' - the most common is by installing kernel header
packages.

If those kernels are removed, then check the U-U logs in /var/log to
ensure that U-U is really operating.

A bug report is an awful place to try to troubleshoot in this way. If
you open a thread on UbuntuForums, we may be able help you better.

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https://bugs.launchpad.net/bugs/1357093

Title:
  Kernels not autoremoving, causing out of space error on LVM or
  Encrypted installation or on any installation, when /boot partition
  gets full

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