Super Duper made smart links instead of copies??
 

So I upgraded my MPB from Snow Lepoard to Lion last night, which turned out to be a big mistake for me. Luckily (or so I though) I had made a full backup via SuperDuper before starting the upgrade process.

When I went back to retrieve some files in my home directory, I found only soft links that pointed back to my (bad) files.

I've never seen SD do this before...what did I screw up? I simply told it to do a full copy, as usual.

I don't think you did - it sounds to me like you made a Sandbox, not a Backup.