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Restart (kill, then start again) Nautilus and see if it helps? Or run 'nautilus' from a terminal and see if you get any (informative) output when trying to click on the items..
If it's only on some (maybe custom) menu items, make sure you have the software installed that the items should run---or if it doesn't work with any of them (or with such things as Cut or Copy), try resetting your gnome/nautilus-related configuration by creating a fresh new user.
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