This issue is something I have had and on the four or so times when it was produced SuperDuper was not involved. I was running 10.4.10 and had upgraded OnyX to the latest version that was 10.4.10 compatible, one task I had OnyX perform was to "Reset LaunchServices Database". After the reboot (which OnyX needed straight away) I had generic icons in my Dock, like the Jpeg Icon and PDF Icon, hovering my cursor over these icons gave the applications name, however clicking these files opened up some random file or picture. At first I thought it was related to ClearDock but after removing that App/Hack I still had the problem. It's defenitly something in 10.4.10 and is not caused by SuperDuper.
I have since done an Archive and Install to go back to 10.4.9 as that was not the only issue I had (I won't rant here about Airport
)