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I'd have to suggest an archive-and-install...
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Good advice, but I'd like to make a solid effort to figure out what's wrong before blotting out the evidence with a reinstall. Without knowing what caused it, I could be back in this situation at any time.
One more symptom...
This does not turn in the log every time, but was logged to the Console two of the times when SD froze.
12/21/10 3:35:00 AM com.apple.launchd[1] (0x10cf90.cron[24611]) Could not setup Mach task special port 9: (os/kern) no access
The timing is way beyond coincidence. It is certainly associated with the launch of SuperDuper for the automated backup.
From what I can glean, this error pops up when there's a bad shell command in a crontab file.