[dnanian]

I'm really not sure why your desktop would be different, given this. It's possible that the preferences involved are not fully written to disk at the time the backup is done, or that they're in a state that causes that particular item to be reset. I'm trying to reproduce it here but haven't been successful.

Do you have any accounts other than this one? If not, try creating one. Set the desktop for that account, then log out of it. Log back in to your main account and do the copy. Boot from the backup, then try logging into the account that was logged out when you did the copy... is the desktop correct for that account?