Cannot start up except with internal disc

I've been having a few irritating problems with my start-up items - various crashes, some not opening, etc., so I went in to the library to delete the prefs. There were 2 prefs that will not delete nor move to the trash -- checking Info they say I have indeterminate permission. Disc Utility says HD is OK, but I wanted to be sure and tried using DU on the Snow Leopard Install disc. It ill not boot up. Next I tried Prosoft's Drive Genius; it won't boot either. I have tried using Command-C, Option and Syspref Start up disc; it always goes to the grey screen then hangs. Help please?
Sass

You cannot move pref files straight to trash. Drag to desktop first, then you can delete.
If you can't start from the install disk, first make sure it's the correct one. If it's a disk for a system update, then find the original startup disk that came with the computer and try that one.

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