AppleJack:Troubleshooting Tool for Macs

I have had a lot of unfixed permissions in Disk Utility. When I found
Applejack I thought that my problems were over. They were actually just
beginning. After running Applejack in Single User mode, my permissions
were NOT fixed. I ran it again and they still weren't fixed. I ran
everything else, and the mem test, then exited to reboot. I could not
reboot but continued to get a multi-national message to shut down the
computer. After trying that several times with no luck, I was able to do a
Safe Boot. Hoping that that had fixed the problem, I rebooted with the
same error message. I once again rebooted in Safe Mode and used my Leopard
Disk to reload Leopard. Then I had to spend the time reloading all of the
updates. No I have to find all of my printer install disks, etc. WHat is
Applejack doing? I see that others have had the same problem. I would
like to send you the log, but I can't find it on my system. I feel that
this problem is a black eye for Applejack. How can we get this problem
fixed?