I have updated the system several times and it dos not clear the notification.
Debian Jessie, currently updated.
uname -a results:
Linux linus 3.14-2-amd64 #1 SMP Debian 3.14.13-2 (2014-07-24) x86_64 GNU/Linux
Please let me know waht other information you need.
We moved the upstream bugtracker to GitHub a long time ago. If this issue still affects you please re-create the issue here: https://github.com/hughsie/PackageKit/issues
Sorry for the impersonal message, and fingers crossed your issue no longer happens. Thanks.