Ubuntu – Why Does Software Updater Say No updates Available, but apt-get upgrade Shows updates available

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'

Ubuntu Software does not refresh immediately after you update software from the terminal or using the Software Updater. To test this I updated my software from the terminal using sudo apt update && sudo apt upgrade and then copied the list of packages that were updated. Then I opened Ubuntu Software and saw the same screen as your first screenshot which showed the same two updates were available. When I clicked on OS Updates I saw the same list of packages that I had just finished updating from the terminal. When I clicked the Install button, Ubuntu Software did nothing, but OS Updates disappeared from the center pane.

Because of the confusing delay in showing software updates that have already finished in Ubuntu Software, I recommend updating packages using either the Software Updater app or the terminal instead of Ubuntu Software.