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Dave,
I had several files on my second drive at the time of the cloning. Initially, I was just going to Backup-All Files from the smaller drive to the larger drive. I read that I was about to erase the second drive in this process. I was able to change this using the options button. Prior to the move, I created a new folder called Drive 2 on this drive. The drive itself was called Macintosh HD 2. I moved all to the files at the root level of this drive into the Drive 2 folder. I also manually dragged my home directory from the Users folder of my boot drive to create a backup prior to cloning. I did not want to lose any documents or lose the ability to open any docuements if something went wrong. I set the options to allow files on the target disk and ran the Backup-All Files with SuperDuper! I took the dog for a walk and came back to find everything working perfectly! All of my files were perfect. Today, I ran Software Update knowing that Apple had released a security update as well as an Airport update. The Software Update application asked me to authenticate with name and password, then delivered the error message concerning permissions for com.apple.SoftwareUpdate. I ran Disk Utility to repair permissions. The update still reported the same error. I tried restarting the computer. Same error. I used Find to search for com.apple.SoftwareUpdate setting it to search for both visible and invisible files. It found the file in 3 locations. One was in username:library:caches:, the second was in harddrive:library;caches:, and the third was in harddrive:drive 2(the folder I had created):users:username:library:caches. When I saw the drive 2 directory reference I thought it might be interferring with software update. I deleted the users folder (my backup copy) from the drive 2 folder and software update ran fine. I am certain that I had run software update after using SuperDuper!, but this is the first time any new software had been available to install. Thanks again for your prompt and thorough assistance.
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