Wierd system behavior after software update

Question

For some reason I got this great idea to reinstall my system from scratch, last week.
I did two identical, redundant backups...both with Carbon Copy Cloner, onto 2 different external drive partitions.
Then, I reformatted my aluminum powerbook g4 HD and did an OS 10.5.6 clean install.
Before the install, i used Disk Utility to ensure the SMART status was OK.
It was.
Immediately after that, I did a software update, updating it to 10.5.8.
Next, I use Migration Assistant, to restore all my docs and apps from a clone of my original HD that I had made with Carbon Copy Cloner, on an external drive.
Reboot was OK and all my files and apps were back.
Then, being a diligent Mac user, I ran software update again, and saw that there was an apple security update and some other updates that needed to be installed.
I went ahead with that.
Now the mac won't boot...the spinning gear runs for 2-3 minutes, then all i get is the grey Ghostbusters circle with a slash through it.
But If I put my original system 10.5.6 installer CD in the slot, and reboot, System 10.5.8 restarts from my HD, after which I can then remove the CD from the Mac and everything works fine.
Except that, for every restart, I have to use the Installer CD.
And now I'm afraid to ever update the OS again.
I went back and did the whole thing over again in the same order...with the same results.
The system apparently finds something on the CD, that it needs, so it can start from the system 10.5.8 that's installed on my HD.
That's wierd.
In one sense this suggests to me that I was probably right in thinking that a clean system install was a good idea; it seems like there might be something awry in the old system, since as soon as I do the Migration Assistant, any further software update, hoses the OS.
About This Mac reports that I'm using:
System Version:          Mac OS X 10.5.8 (9L31a)
Kernel Version:          Darwin 9.8.0
Just wondering if this might ring a bell with some Genius out there, who might have a simple fix, versus re-clean installing, then software updating to 10.5.8, then reinstall all my apps, then do the security update, and hold my breath.....over and over again, until I hopefully hit the right  combination.
Or, I guess I could just restore one of the redundant backups, and forget about a clean system install...but now I'm getting stubborn. 
I WANT that clean install! :-)

Answer 1

First, I would install the 10.5.8 combo update, which contains all fixes for Leopard. It's available from http://support.apple.com/kb/DL866 . Often Software update does something odd, and applying the combo update fixes it. Repair permissions first, apply the combo update, then repair permissions again. You might try this with the system in the state it is today to see if it brings everything back into sync.