Comment 7 for bug 494096

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!