Much more technical diagnoses that I was about to write, but this is
exactly the behavior I've noticed as well.  Well done, sir.

I have Pidgin set to flash if I have a message needing attention as
well, and so I intentionally look in the upper right corner when I see
the flicker.  Damned annoying.

-- 
nm-applet causes flicker by needlessly changing itself
https://bugs.launchpad.net/bugs/229559
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