Upgrading release of Ubuntu some programs are not re-integrated

     I recently updated Ubuntu 'Jaunty' x64 Bit. (Updated 10/22/2009 - most recent BIG update) when the update was finished I had to go back and re-install a couple of locally installed programs and a few firefox extensions. Apparently programs that are installed with GDebi package installer locally were not re-integrated with the update. One of the programs was Sun's Virtualbox, version 3.0_3.0.8-53138_Ubuntu_jaunty_amd64.deb. It is the only package that I installed without the Synaptic Package Manager because I wanted the new x64 support. Another really weird one was in Firefox. The extension 'FEBE', firefox extension backup extension, and CLEO, were also affected by the update; they had to be re-installed over themselves before they could work right.
     It seems updates that have to re-write the kernel do not take into account locally installed packages. I have also noticed that the Computer Janitor considers these programs obsolete or uninstalled. It would be nice to update without having to re-install virtual machine programs and Firefox extensions. It would be nice to be able to tell the computer janitor that certain programs are OK and to not display them, or mark them as user installed and OK.
     Well that is about it as far as updates. On another note...when I choose "Report a problem" from the menu....nothing happens!