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.
To install new versions of Virtualbox a good way is to follow the official installation page:
In practice you have to add this line to /etc/apt/sources.list
deb http://download.virtualbox.org/virtualbox/debian raring contrib(change "raring" with the name of your release)
Then do this command to save the gpg key:
wget -q http://download.virtualbox.org/virtualbox/debian/oracle_vbox.asc -O- | sudo apt-key add -and finally install it by doing this:
sudo apt-get update
sudo apt-get install virtualbox-4.2
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