I tried switching to a TwinView configuration but unfortunately I can't
get it to work correctly in terms of positioning & maximizing windows
(which is more painful than it sounds - everything appears, by default
between 2 monitors including notifications and popups)

Thinking it might be MetaCity related I tried installing kubuntu to see
if that fixes the problem but the same issues happen.

I've found that if I click carefully with my mouse (wait for windows and
web pages to load completely before trying to interact with them, try
not to use the mouse as much as possible) I can mostly avoid causing the
problem for a couple hours of work time, but inevitably eventually
something will happen that triggers the bug.

On the upside I'm polishing up on all my keyboard shortcuts...

-- 
X.org will intermittently stop responding to mouse clicks after Ibex Upgrade
https://bugs.launchpad.net/bugs/296167
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