I'll open up a compiz task (I assume you are using compiz, let me know
if you are using something else such as metacity), though I can't
reproduce the issue so I can't confirm it. If it was reproducible for a
large set of users I think it would quality as a paper cut as the newly
opened window should have focus regardless of an always on top window
existing.
** Also affects: compiz (Ubuntu)
Importance: Undecided
Status: New
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New windows don't get focus when other window is "always on top"
https://bugs.launchpad.net/bugs/392241
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