Can you try the following when it works:
$ xmodmap -pp > ~/xmodmap-pp
$ xev | grep -i button
Put the mouse cursor into the rectangle and push your mouse buttons. A left 
click generates button 1 press and release events and a right click generates 
button 3 press and release events.

And the following when it fails:
$ xmodmap -pp > ~/xmodmap-pp_tmp
$ xev | grep -i button
Does a left and right click generate the right events?

Then run the following command:
$ LANG=C diff -ns ~/xmodmap-pp ~/xmodmap-pp_tmp > ~/xmodmap-pp_diff

Attach ~/xmodmap-pp, ~/xmodmap-pp_diff and the requested information to
the bug report.

-- 
Intermittent mouse flakiness (works on some boots)
https://bugs.launchpad.net/bugs/120043
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