I'm also experiencing this bug, but it does not seem to be limited to gtk 
programs, Konsole is also affected.
I am unable to give you steps to reproduce the bug, though it keeps happening.
The bug occurs under both KDE and XFCE.

SCIM/SKIM seems to be involved, as killing it after this bug occurred
completely crashed XFCE (ctrl-alt-backspace was required to get back
into usable state)

I will keep them killed from now on to see whether this affects the
occurrence of the bug.

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Some gtk+ programs (gvim, gedit, gnome terminal, firefox...) sometimes do not 
receive keyboard inputs
https://bugs.launchpad.net/bugs/40137
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