I can confirm this. It started happening in 9.10 for me too, and it's
still happening on my freshly installed Lucid.
It's rather annoying because the "lost clicks" randomly affect the
applications below the focused window: they may e.g. close an
application by hitting its [X] button, or they may even delete stuff by
clicking on some Cut/Delete/Paste button, and the user may not even
notice it, as the application where that happens isn't focused!
** Changed in: metacity (Ubuntu)
Status: New => Confirmed
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Clicking the title of a window is bringing a window underneath it into focus
https://bugs.launchpad.net/bugs/494096
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