Clone & ?folder

Question

I had to clone the entire contents of a TiPBG4 10.3.8 to another machine. I used Target disk mode, wiped the target disk clean and repaired permissions&priviledges on the Source disk before starting the cloning process (CCC 2.3).
The process seemed seemless and perfect, except with continued use, certain things don't won't, or don't work correctly.
First odd behavior; ever so infrequently, during the startup process, I get a folder with a ? icon. Maybe once every 15 startups and then maybe I won't see it for days.
Second behavior; there are folders or files that did not transfer the proper read/write pemissions (all applications seem to work fine) and I have to manually change the file's read/write owner. The problem files/folders that should have my user id, have instead "System" as owner.
Any ideas on what went wrong with the cloning process?? It's a pain in the butt to manually change these problem files.
Third problem; a file that contains 1000's of files & folders lost its custom icon after the transfer. Even after numerous attempts to paste in the desired icon, no luck. This file has not been indexed. What role does indexing play?
Thanx for the hints/help.

Answer 1

Open the Startup Disk preference pane, select the desired startup volume, click on the Restart button.<<</div>
Not sure what you want here. The correct startup file/volume has been always selected.
When you cloned using CCC did you take care to check the switch "Make Bootable" under the Target Disk Options?<<</div>
Yes. Otherwise, would I be able to boot from the newly transferred OS??
Did you take care to check the target disk with Get Info to be sure the box "Ignore permissions on this volume" was UNChecked?<< </div>
I doubt it. There was no operating system installed, simply a formatted HFS+ disk. And I don't remember if CC asked before the process started. I hope I mentioned that my first attempt to install 10.3.8 on top of 10.4.3 would hang during startup. Hence the need to erase the disk.
And, did you verify that the permissions on the target volume were correct?<<</div>
Would this be a process to check after the cloning? If you mean did I use DU to verify p&p on the Target after cloning, I'm 95% certain I did. I certainly have run DU several times since the clone was completed.
The loss of the custom icon may have been due to a problem in the cloning process. Perhaps the next time you might try cloning with Disk Utility by using the Restore option.<<</div>
Never occured to me that DU has the capability to complete such an operation. I cloned the complete contents of the Source disk, including System9. The curious problem with taking the bootable System9 to the target was the first time I used either Classic or booted into System9 (I don't remember which I did) required that I enter the Conflict Catcher registration number, as if I had just installed the software.
I expect I'll be moving this specific operating system and files to faster Travelstar HD after I get the PB display repaired. I'd like to avoid a similar fate.