Starting from OS X 10.7 (Lion), running the Disk Utility app. to fix disk permissions, doesn't include fixing the file permissions on a user level, only the System specific files (Like the global Library etc.).

This may cause issues, when installing 3rd-party apps. to the user home directory, as your local Library is just as prone to incorrect permission settings as the global one.

Repairing permissions in Lion and beyond

As the functionality is no longer in Disk Utility, how do you fix permissions beyond Lion ? Now, the feature is located inside boot Repair Utilities. Here’s how to access it.

  1. Restart (Mountain) Lion and while booting, hold down the Command and R keys.
  2. You Mac should now boot into Repair Utilities mode.
  3. In the topmenu of the screen that appears, click the Utilities item then select Terminal.
  4. A Terminal window should appear, type resetpassword into it and hit Return.
  5. The Password reset utility launches, however we're not really interested in resetting the password or anything like that. Instead, click on the icon for your Mac’s hard drive at the top. From the drop-down positioned just below it, select the user account where you are having issues.
  6. At the bottom of the window, you should see ‘Reset Home Directory Permissions and ACLs’. Click the Reset button, and the application will reset all ACL's in the home dir to default, repairing all Library permissions etc.

Once the repair is completed, you should be able to restart, using the Apple top menu.