Here is a nice mosaic of the problem.
This started by itself after an update a while back.
I have it on both of my computers and on one of them I have installed only a few command line tools like screen and SSH.
I really don't see what I could have done to make this happen.
Suggestions?
Update: If I mouse over the icon, the black dot disappears until I move the cursor away.
BONUS.: Extra geek cred to whoever can tell were the icon bellow Firefox comes from
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