Happens here too. I think the author's intention was to make the window
topmost and a tool window at the same time - but he forgot about the
topmost thing so the window lurks near the bottom of Z-order on a
crowded desktop. The only way to get to it is minimizing other windows
one by one. Confusing at first, even more to novice users I guess.

Unchecking "Keep child windows always on top" and restarting eliminates
(or sidesteps) the problem.

I don't know Ubuntu policies about those minor bugs - is there any hope
it will be fixed as an update to Feisty (at least by unchecking "keep on
top" by default)?

-- 
qjackctl main window doesn't show on fiesty
https://bugs.launchpad.net/bugs/114720
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