I asked from the upstream author if this is known issue, and he said
this:

    Ubuntu drops privileges, but their config is often not really up
    to that. Keep running as root for a test and check if the problem
    re-occurs. I guess not.

So I commented out the $PrivDropToUser and $PrivDropToGroup lines from
/etc/rsyslog.conf and the problem disappeared. The next thing is to
solve how the config should be made "up to" dropping privileges to avoid
this issue.

@William Hidden: Have you reported a separate bug for you problem? Could
you try if running as root helps to your issues, too?

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https://bugs.launchpad.net/bugs/672953

Title:
  rsyslog stops writing to fifo on HUP

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