Hi, dlm. Why do you think the system isn't blessed? From what you've said, I'm guessing you're assuming that, because the system folders don't have "special" icons, you don't think it's blessed. But, Finder doesn't actually put the "special" icons on unless it's the boot drive, so that's not a telltale sign.
Could you locate your SuperDuper!.log (in Library/Logs off your home folder) and send it to support -at- shirt-pocket.com? I'll take a look at what happened, and we'll diagnose the problem from there.
Sound reasonable?
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--Dave Nanian
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