The exact same bug occurred to me when updating from 12.04 to 12.10.
On my machine also /etc/cron.daily/apt is not set executable.
So, I think, unfortunately the bug still exists?!
** Changed in: update-notifier (Ubuntu)
Status: Expired => Confirmed
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https://bugs.launchpad.net/bugs/390319
Title:
Ubuntu does not automatically check for updates, even when set to
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