Michael and I have now refined the test case to make it easier to run:
1. Install Ubuntu.
2. Log in to the new Ubuntu installation for the first time.
3. In “Software Sources” > “Updates”, choose “Check for updates: Daily” and 
“Install security updates without confirmation”.
4. At a terminal, run sudo /etc/cron.daily to trigger the background 
installation of security updates.
5. Once cron.daily has exited, run killall update-notifier && NO_FAKE_STAT=1 
faketime -f +1d update-notifier to test the update-notifier behavior. Update 
Manager should open, displaying only non-security updates.

If this works, but the steps in the current description still do not,
then I guess the problem is with step 4: /etc/cron.daily isn't being
run, or the updates are failing when being run from cron.

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security updates not installed daily as configured
https://bugs.launchpad.net/bugs/549217
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