If it helps, here is the behavior I am seeing:

1. Problem is sporadic. Sometimes it happens frequently (and is
extremely annoying), other times it happens rarely.

2. When it happens, it appears that some X window (I say "some" to mean
"any" as far as I can tell) that has just interacted with the mouse (and
perhaps performed some kind of a grab) doesn't release the grab. In
other words, if I right-click on some other screen location that is
above a different widget, and the last thing to have grabbed the mouse
has a context menu, I'll get the context menu for that last item instead
of the mouse events being passed to the item I'm trying to click.

3. Sometimes, furiously left and right clicking, Alt+Tabbing, etc.
appears to clear the error. Other times, I have to hunt down the widget
that has the cursor and click it with alternating buttons to try and
reset the mouse grab state.

It's been years since I've done anything with Xlib, but if I had the
time to try and find this bug, I'd start looking for reasons why random
grabs aren't being released.

-- 
Mouse clicks stop working sporadically
https://bugs.launchpad.net/bugs/41301
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