I recently downloaded Virtualbox version 4.2.12, and I clicked the .deb file, which brought up the Ubuntu Software Center. I clicked upgrade as I had a previous version installed, and it did it successfully. Then when I rebooted Ubuntu, I got a serious error from Package Manager saying: "Unknown Error:'' (E:The package virtualbox-4.2 needs to be reinstalled, but I can't find an archive for it." Then it goes on to say: "This usually means that your installed packages have unmet dependencies." Strangely, The Ubuntu Software Center didn't give a notification about unmet dependencies. Since then, Ubuntu Software Center and Package Manager can't Update, Install and Uninstall Software.
I also recently upgraded to Ubuntu 13.04 the day that it came out, if that helps.