My understanding is, that the automatically installed flag is set when
the package comes in as a dependency and was not specified by the user
directly.

As the problem cannot be reproduced, maybe a trace can be found in
the /var/log/dpkg* log files on your system. If the logs are still
around, you might be able to check what other packages were installed
close to the time of conky-all. The output of
$ zgrep -A5 -B5 conky /var/log/dpkg.log*
might contain enough information.

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https://bugs.launchpad.net/bugs/708803

Title:
  [Maverick] autoremove removes package which is required

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