Comment 18 for bug 53868

@Marktrix: Thanks, could you please try the following:
$ sudo /usr/share/update-notifier/notify-reboot-required
$ sudo touch /var/lib/update-notifier/dpkg-run-stamp

and check if there is a "reboot required" notification (and icon) coming up?
Could you also please add the output of:
$ ls -l /var/lib/apt/periodic/

Thanks,
 Michael