When I press system cog and "Shutdown.." it just freezes some windows and shuts Ubuntu down. I would expect to see the options to Restart or Shutdown.
It happened after some work with terminal, probably some packages.
P.S. if it could be related I got this at the same time as this error Missing System Settings after removing some packages and non of the answers help
Ubuntu 17.04
Sounds like your desktop software got slightly messed up. As a quick fix, this should work
sudo apt-get install ubuntu-desktop
Without knowing details of what you've been working with (version of Ubuntu, the meaning of "some work with terminal", etc), could you try restarting the window manager with following command
sudo systemctl restart lightdm
(Assuming you're running the latest version that uses systemd init instead of upstart)
