I'm seeing this since Intrepid with Metacity.  Desktop effects are
disabled.  I have a dual-monitor ATi setup.  I am using the Clearlooks
theme.

I will be working in an app and select a file on my desktop to rename or
delete using keyboard shortcuts and the operation is performed in the
app instead.  I have not discovered what triggers this behavior.

I noticed that when this happens, the Window Decorations of the last app
used stays active even when selecting a file on the desktop.  If I have
multiple windows open and change the focus between them, the desktop is
not granted focus.

One workaround I've found to give the desktop focus is to use the Show
Desktop applet in the panel.

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focus does not return to desktop after opening and closing a file on it if 
anther window is open
https://bugs.launchpad.net/bugs/268963
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