I too, have had an issue after restoring a disk with SuperDuper as this user described earlier:
http://www.shirtpocket.com/forums/showthread.php?t=2687
I am using ver. 2.14 to backup a pretty standard OS-10.4.10 disk with multiple users. I noticed that one of the users looked OK but 4 others had strange Icons in the dock that referenced obscure image files or text files mostly within the System. This has happened on two separate occasions so far.
(All machines backed up and restored to are Intel.)
EDITED: Sorry for the multiple post. When I first visited the post I mentioned above, my browser showed no replies....