The problem is that your UID/User ID might be different on the new volume than it was on the old one. For other users who might be reading this --
do not do it this way. Migrate when
first prompted to "Copy from another Mac" during the first boot after install.
Anyway, I don't know why these folders would become visible on you, especially since you just migrated, and never ran SuperDuper at all (not that running SuperDuper! would do this).
You can set a 'hidden' attribute for each folder if you have the Developer Tools installed. If so, use
Code:
sudo SetFile -a v path-to-the-file
That removes the 'visible' attribute from the file you specify.