I just experienced this problem on my Lenovo ThinkPad X200, using the laptop 
keyboard and a Logitech M705 USB mouse.
- Menus in the Gnome panel were highlighted, but would not open.
- I could click to change, open or close Chrome tabs, but not click on text 
fields etc. or switch to other applications.
- Scroll buttons and some keyboard shortcuts (like <Super><Button5> to rotate 
Compiz cube) still worked and I could switch to a console (<Ctrl><Alt><F1>) and 
reboot the system.

I have no idea what caused this and no traces in dmesg, /var/log/messages nor 
/var/log/Xorg.0.log.
It happened as I was using gvim, trying to figure out some builtin 
keyboard-shortcuts.

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Mouse and keyboard become unresponsive on Asus Eee PC 1005HA
https://bugs.launchpad.net/bugs/569354
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