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35a32c5
(Get the code!)
On a Mythbuntu (Xubuntu 10.04 Lucid) system I noticed this begin with 2.6.32-29.
Booting to 2.6.32-28 resolves the issue.
I cannot see anything in the Changelog that indicates a change that would affect the input events.
The effect is as described by the original reporter - focus is captured by one window or application, and despite being able to click on other windows or the system menus, there is no response. I found that by clicking the middle and/or right buttons in the window that has captured focus, and without dismissing the resulting context menu pop-up, moving to another window or the system menu, I am able to then left-click to select. That gets dicey when the system menu captures focus though, getting out seems more difficult.