I've never had this problem before. I just upgraded to 11.10 and now clicking or dubleclicking a file doesn't cause it to run in its associated program. Clicking works on the unity bar all right, but not on files or folders. I have to right click, and select open. It's a pain!
With the Desktop or your Home folder open, from the menu bar, choose: Edit -> Preferences -> Behaviour and look at the options in the first group of radio buttons.