Comment 6 for bug 1222096

A regular-auto-launch-interval of 0 means that update-manager will launch as soon as updates are available. With update-notifier's lack of support for phased-updates it is likely that the notification is due to an update undergoing phasing which update-manager chooses not to install, hence the message your system is up to date.

One way to confirm this would be to include the output of 'apt-get upgrade' in a terminal.