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I just updated Ubuntu 16 LTS and after the restart I can't use Ctrl Keyboard combinations (Ctrl + C, Ctrl + Right, Ctrl + T ...) in applications anymore (neither left - Ctrl nor right - Ctrl). I'm using a Gnome-3 desktop and here Ctrl seems to work, e.g. in search I can Ctrl + A and the System-Keyboard-Application recognizes left/right - Ctrl presses. It's only in all User-Applications and the terminal that I can't use Ctrl. All other shortcuts seem to work fine, even Ctrl + Mouse-Scroll to zoom.

I have no custom shortcuts.

I wouldn't be sure it has anything to do with the latest update since I also installed a lot of applications since the last restart.

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Turned out to be the application SyncWall (which is otherwise great). Specifically removing the shortcuts did the trick (disabling the function wasn't enough). Don't know why they would conflict and why it only happened after the reboot since I installed the application much earlier and definitely didn't have this problem before.

Such a relieve, this was really bugging me. So I wanted to file a ticket on sourceforge but wasn't authorized by the project admin.

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