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We currently have an option called "Focus Follows Mouse" set, which is different from most other environments. Basically, whichever window the mouse is over is the window which you will be typing into regardless of whether or not it is on top of the screen. The only exception to this rule is if you point to a window which has told the window manager it has no use for a keyboard, like the blank desktop area with the picture of the library in it, in which case the keyboard stays attached to the last window that had it. You can easily see which window has control of the keyboard because it's title bar will be brighter than the others.
This behaviour is configurable, so we might switch it back to the more conventional click to focus model if too many users are confused by it. It was done because we tried it inhouse and liked the feature.