I removed my original patch, as I realised that one of the changes
between versions 0.76.8 and 0.87 of update-notifier is that this bug has
been fixed in 0.87 (if the candidate version of the current package is
itself a security update,it does a 'continue', to process the next
package, and doesn't even enter the loop to find security updates).

That continue could be added between lines 103 and 104 of the version of
apt_check.py in update-notifier version 0.76.8.

-- 
apt-check.py counts security updates twice if pkg in -updates and -security
https://bugs.launchpad.net/bugs/413885
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