Mac Pro- Damaged Disk/Permissions - Disk Warrior unable to fix, please help

Question

Hey, I am really hoping I can solve this over the discussion board. My Mac Pro 1,1, with OSX 10.6.2 installed, has been acting up really badly lately. Random crashes, really slow, and my Radeon XT1900 is about to die, I think; the fan almost never turns off.
But the main issue I'd like to address is my damaged home disk. I booted up from the install disk and used Disk Utility to "Verify and Repair Disk" on my home disk. It said that the "Header has some minor damage," the repair finished and DU reported that it had repaired the volume and everything was fine.
However, after booting up from the HD, I went back into Disk Utility and did another "Verify Disk" to double check. It came up with an error stating: "Disk Utility stopped verifying 'Home' The disk needs to be repaired. Startup your computer with another disk and use DU to repair this disk."
So I booted from the install disk again, ran Disk Utility, and it said that everything was fine. So I booted back from HD, ran DU - only for it to report the same error as before. Why is DU reporting a problem when booting from disk, but it says there is no problem when running from the install disk?
I decided to get Disk Warrior to see if that would help. I used it to "Repair Disk Permissions" and also "Check All Files & Folders". Disk Warrior then stopped saying: "An unexpected error occurred while attempting to perform the file operations. Restart from DW disc and try again. ERROR CODE (2903, -8902)."
Here are some screenshots of the errors from Disk Warrior and Disk Utility (booted from HD). image: !http://img683.imageshack.us/img683/9789/duerror.png!
image: !http://img683.imageshack.us/img683/9269/dwerror.png!
So my main question is: Why, after Disk Utility, running off the install disk, reports that it "repaired - some minor damage to the header," does it then report the "header is damaged" when booted from the system?

Answer 1

Don't rely on just Apple First Aid, or trust it with finding and repairing.
Sorry you had to wait this long to get Disk Warrior.
You should always run DW from another hard drive.
Install a fresh clean copy of 10.6.x on a small 30GB partition for emergency only.
you can use that to boot from to run repairs and maintenance using Apple and Disk Warrior.
Don't bother using DVDs or CD to boot from.
It sounds like you are running DW and DU from hard drives, but not clear which or from where (and when).
Always use the SAME version when repairing permissions, never use an older version OS or of Disk Utility.
CLONE your system. Always have a couple bootable backups.
Choice is Apple Disk Utility Restore; SuperDuper; Carbon Copy Cloner
If a drive does have errors, be ready to restore and have backups on hand if it comes to that.
System (OS and apps) probably only change weekly or even monthly.
You can backup /Users to its own backup partition more often, and use Time Machine plus another method there.
Personally, I tend to run DW directory repair first and sometimes only, and only then check files.
TechTool Pro 5 is what I use for checking files, disk media for weak sectors, and some other problems not covered by Disk Warrior; and, because it can run concurrently on multiple volumes and drives.
It is 'iffy' to verify a live system and get an accurate read of its health, but I'd say Disk Utility is "out of its depths, and league" when it comes to finding and repairing, and for the errors it is encountering on your system.
Isolate the sytem from data and media files and libraries as much as you can and still easy to manage.
Most errors are with system or boot drive.
Radeon X1900 needs to be removed, carefully inspected, and any dust in the vents, air intake portion and exhaust, cleaned out. Right now the only real upgrade there is the ATI 4870 for now (Apple's or flashed).