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After doing the drive repair and directory rebuilding I figured I'd try backing up the original HD to the external (which is what I was trying to do when this all started). Just a short time after starting the "smart update", the external drive gets unmounted and this error came up (below).
I'm not even sure what to say when I call Apple?? Disk Utility didn't reveal any problems, my computer seems to be running properly... but I'm not able to back it up using SuperDuper, and I'm not able to start-up from the OSX DVD. I suspect they'll just tell me to contact the software developer (you) on the backup issue because I don't imagine they know much about SuperDuper.
Here's the log:
| 07:12:06 AM | Info | Did not COPY shared-item /Volumes/Lovebox/private/tftpboot/private/tftpboot because it would have overwritten the original
| 07:12:09 AM | Info | Ignoring /Volumes/Lovebox/private/var/db/volinfo.database
| 07:12:09 AM | Info | Ignoring /Volumes/Lovebox/private/var/db/BootCache.playlist
| 07:12:41 AM | Info | WARNING: Caught I/O exception(5): Input/output error
| 07:12:41 AM | Info | WARNING: Source: /Volumes/Lovebox/private/var/log/daily.out, lstat(): 0
| 07:12:41 AM | Info | WARNING: Target: /Volumes/Lovebox Backup 3/private/var/log/daily.out, lstat(): 0
| 07:12:41 AM | Info | Attempting to copy file using copyfile().
| 07:12:41 AM | Info | Attempting to copy file using ditto.
| 07:12:41 AM | Error | SDCopy: Failed to recover from copy error for file /Volumes/Lovebox/private/var/log/daily.out:
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