Whilst investigating another problem I've just realized that the
behaviour described above for apt-get --simulate update appears to be
caused by the ordering of repos in /etc/apt/sources.list. If the
lucid/karmic security repo is listed first, apt-get --simulate update
reports that there are a mix of security and non-essential updates
required. If the lucid/karmic updates repo is listed first (and the
security updates repo is second), apt-get --simulate update reports that
there are no security updates available but the same number of non-
essential security updates. Altering the repo order will change the
behaviour of apt-get update.

Whether this is a design issue in apt-get, or a race condition, it seems
to be this that causes the disparity between apt-get and update-notifier
(and which will also break Nagios checks using the Ubuntu bundled
nagios-check-apt-updates script for pending security updates, or any
other similar tools that attempt to hook the same reporting mechanism).

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https://bugs.launchpad.net/bugs/674534

Title:
  Update-notifier incorrectly reports security updates (including on login)

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