Hi Helen,
that explains a lot. 😎 It is usually best to install plug-ins and programs for all users by using an Administrator account when installing. That will prevent permission problems.
Is your Aperture application not installed in the Applications folder on your Macintosh HD?
I was puzzled, because your signature still is showing "Aperture 3.1.3". If that is true, you have missed many updates and bug fixes. The most recent Aperture version for "Mac OS X (10.6.8)" would be Aperture 3.2.4.
But Software Update will not show the updates, if Aperture is installed in a local Applications folder and not in the system wide "Applications" directly on your HD; also it should be named simply "Aperture" and not Aperture 3 or something similar.
Regards
Léonie