I have noticed this behavior accross several versions of ubuntu and
accross two different laptops and my desktop. I first thought it was a
KomodoEdit bug since it always started while in Komodo (but as a
developer I spend the majority of my time in either KomodoEdit or
Firefox), I then thought that it was a Gnome clipboard manager bug since
it always affected copy-and-paste procedures. Since I have also
determined that it also affects the virtual consoles as well it no
longer thing that it is a gnome centric issue.

I seem to bring it on my doing a lot of control key activity since it is
usually proceeded by long periods (a full minute or more) of continuous
pressed control key. But I can not reproduce at will.

Though possibly not Gnome / X related, I find that restarting X fixes it
(crtl+alt+bksp)

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Ctrl-key stuck in Gnome after continued browsing
https://bugs.launchpad.net/bugs/237604
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