I am having a similar problem. While having multiple applications open, usually 
Firefox, Evolution, and a folder, the Gnome desktop freezes:
Mouse clicks on the navigation bar are unresponsive.
I can use Alt-Tab to switch between windows.
Applications and folders are responsive.
Desktop icons are not responsive.
The desktop chooser and Desktop Icon are not responsive to mouse clicks.

I have a hunch that Boinc may be involved in the problem. I uninstalled
Boinc using the software chooser but have seen it still in the list of
processes.

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Firefox hangs gnome desktop
https://bugs.launchpad.net/bugs/523528
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