[dnanian]

We don't touch the files on the source except to read them, Bob, so I can't see how your prefs (or other files) could possibly have been changed due to the copy itself... perhaps some other application you were running did this?

(Any "Repair Permissions" done in SD! simply runs Disk Utility to do the repair, and that doesn't touch user files -- just OS and applications that have receipts in /Library/Receipts.)