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Disk Utility can't repair permissions

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For the first time I neglected to repair permissions before security upgrade and now I find I can no longer repair permissions. Everything goes as normal until about 75% done and then it just freezes. I have tried running it from the install CD but it does the same. I used the disk repair and got this error message;
ERROR: The underlying task reported failure on exit (~9972)
1 Volume could not be repaired.
Computer otherwise OK. AHT reported all OK.
Is this the start of an HD failure or some querky software malfunction? Help needed!
G4 867 MDD   Mac OS X (10.3.9)   Extra 120Gb HD, 1.75Gb SDRAM LG 4163B Superdrive

Answers

If my HD has developed a bad sector then surely a clone will not work?
My best guess is that the cloning would fail when it tried to access the data that's referenced in the bad directory node. I've had similar problems when trying to copy files when there were directory problems. You may not have a bad sector per se, but certainly the directory record is damaged in such a way that Disk Utility can't reconstruct the record.
If I moved all my APPS folder to another HD and then did a Zero and format on this one could I then still use the APPS folder with a new install by repairing permissions?
You have to remember that apps store files in other locations - particularly in the /Library, /System/Library/ and /Users/username/Library directories. While you can copy the Applications directory to another drive, you're liable to miss supporting files the apps are going to look for. Since there's no real way to determine what the damaged directory is referencing, you'd be chancing something's going to get missed and leave you with apps that won't run. The only way I've ever been able to find what directory erorrs were pointing to was to copy files to another drive one chunk at a time until I found the offending directory and then narrow down the search by copying files individually. Given the nature of OS X to store files in directories that are otherwise hidden from the user, this can be a complicated and tedious process.
Since Disk Utility running from the install disk can't repair the damaged directoy record, I'd go to the Disk Warrior repair strategy next.
-Douggo

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