Ubuntu – Invisible software updates list in Software Updater

Hm, this seems to be exactly what PhasedUpdates are. Also check out http://www.murraytwins.com/blog/?p=127 and http://lwn.net/Articles/563966/.

To summarize links above:

• Ubuntu quietly introduced a new mechanism in its 13.04 release that progressively rolls out package updates, pushing each update to a small subset of the total user base first, then steadily scaling up, rather than publishing the update for everyone simultaneously.
• On the client end, phased updates are implemented in the update-manager tool, which is Ubuntu's graphical update installation application. The other methods for updating a package, such as apt-get, are not affected by the phased update plan.
• update-manager generates a random number between zero and one for each package, then compares it to the Phased-Update-Percentage value published on the server for that package. If update-manager's generated number is less than the published percentage, then the package will be added to the list of available updates that the user can install. Dependencies for a package are pulled in automatically.

• One can opt out of the Phased Update process by adding the following to the configuration file /etc/apt/apt.conf:

  Update-Manager::Never-Include-Phased-Updates “True”;
  

Here a one-liner to print all packages with the Phased-Update-Percentage tag:

apt-cache show ".*"|sed -r '/^Package:/h;/^Phased-Update-Percentage:/{H;x;s/\n/\n\t/;p};d'

This is a common thing which is simply solved. These commands clear the "phantom" or "hung" lists and may have to be used again as needed in the future for similar bug:

sudo rm -rvf /var/lib/apt/lists/* 

and then:

sudo apt-get update

You may need to reboot computer for it to effect completely by typing:

sudo shutdown -r now