[dnanian]

Macgator:

When you made the copy, did you use "Backup - all files"? It's quite strange that the external volume -- a full copy -- would work fine, but the internal one wouldn't.

Hopefully, you haven't messed with the external copy too much... we can try to see what's going on there.

Please contact support, and when you do so, include the SuperDuper!.log from your Library/Logs folder off your Home. (The one when booted from the external, working drive would be best...)