This sounds like for some reason your permissions are mixed up.
Could you please run (in a termianl):
$ ls -l /etc/apt/apt.conf
It is most likely that
$ sudo chmod 0644 /etc/apt/apt.conf
fixes the issue.
Its not a bug in update-notifier I close it therefore.
Cheers,
Michael
** Changed in: update-notifier (Ubuntu)
Status: Unconfirmed => Needs Info
** Changed in: update-notifier (Ubuntu)
Status: Needs Info => Rejected
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update-notifier / apt-get
https://launchpad.net/bugs/45616
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