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Oops, I might have blown it. Before reading this message I did repair the disk as you suggested but I also repaired permissions.
Here's the full log below. I just repaired permissions and did maintenance on the source (using Onyx), and tried backing up again, but still no luck. I see that the bad file descriptor is related to an image file in my Aperture library (Apple's professional photo editor).
Thanks again for your help.
| 12:08:59 PM | Info | SuperDuper!, 2.1 (77), path: /Volumes/Lovebox/Applications/SuperDuper!.app, Mac OS 10.4.6 build 8I127 (ppc)
| 12:08:59 PM | Info | Started on Sun, Apr 30, 2006 at 12:08 PM
| 12:08:59 PM | Info | Source Drive: Lovebox, mount: /Volumes/Lovebox, device: WDC WD1600JS-41MVB1, interconnect: Internal ATA, file system: "Journaled HFS+", OS: 10.4.6 (8I127), capacity: 148.93 GB, used: 85.54 GB, directories: 71773, files: 308516, ejectable: NO, ACLs: Disabled
| 12:08:59 PM | Info | Target Drive: Lovebox Backup, mount: /Volumes/Lovebox Backup 2, device: WDC FireWire/USB2.0, interconnect: External FireWire, file system: "Journaled HFS+", OS: 10.4.6 (8I127), capacity: 111.67 GB, used: 88.44 GB, directories: 72548, files: 310565, ejectable: NO, ACLs: Disabled
| 12:08:59 PM | Info | Copy Mode : Smart Update
| 12:08:59 PM | Info | Copy Script : Backup - all files.dset
| 12:08:59 PM | Info | Transcript : BuildTranscript.plist
| 12:09:00 PM | Info | PHASE: 1. Prepare to Copy Files
| 12:09:00 PM | Info | ...ACTION: Preparing Lovebox
| 12:09:00 PM | Info | ......COMMAND => Verifying the integrity of volinfo.database
| 12:09:00 PM | Info | volinfo.database OK
| 12:09:00 PM | Info | ......COMMAND => Enabling permissions on Lovebox
| 12:09:00 PM | Info | Refreshing Disk Arbitration ...
| 12:09:00 PM | Info | ......COMMAND => Verifying that permissions are enabled for Lovebox
| 12:09:00 PM | Info | Permissions on '/Volumes/Lovebox' are enabled.
| 12:09:00 PM | Info | ...ACTION: Repairing permissions on Lovebox
| 12:09:00 PM | Info | ......COMMAND => Repairing permissions on Lovebox
| 12:09:04 PM | Info | parent directory ./Users/Shared/SC Info does not exist
| 12:09:22 PM | Info | Started verify/repair permissions on disk disk1s3 Lovebox
| 12:09:22 PM | Info | Determining correct file permissions.
| 12:09:22 PM | Info | The privileges have been verified or repaired on the selected volume
| 12:09:22 PM | Info | Verify/repair finished permissions on disk disk1s3 Lovebox
| 12:09:22 PM | Info | ...ACTION: Preparing Lovebox Backup
| 12:09:22 PM | Info | ......COMMAND => Enabling permissions on Lovebox Backup
| 12:09:22 PM | Info | Refreshing Disk Arbitration ...
| 12:09:22 PM | Info | ......COMMAND => Verifying that permissions are enabled for Lovebox Backup
| 12:09:22 PM | Info | Permissions on '/Volumes/Lovebox Backup 2' are enabled.
| 12:09:22 PM | Info | ......COMMAND => Verifying that Lovebox Backup ACL support matches Lovebox
| 12:09:22 PM | Info | ......COMMAND => Disabling Spotlight search indexing on Lovebox Backup
| 12:09:22 PM | Info | PHASE: 2. Copy Files
| 12:09:22 PM | Info | ...ACTION: Copying files from Lovebox to Lovebox Backup
| 12:09:22 PM | Info | ......COMMAND => Cloning Lovebox to Lovebox Backup
| 12:09:22 PM | Info | Copying different files with delete using script: /Users/kavio/Library/Application Support/SuperDuper!/Copy Scripts/Standard Scripts/Backup - all files.dset
| 12:09:23 PM | Info | Loading 19 commands from copy script /Volumes/Lovebox/Applications/SuperDuper!.app/Contents/Resources/Copy Scripts/Exclude system temporary files.dset
| 12:09:23 PM | Info | Loading 6 commands from copy script /Volumes/Lovebox/Applications/SuperDuper!.app/Contents/Resources/Copy Scripts/Exclude system cache files.dset
| 12:09:23 PM | Info | Loading 1 commands from copy script /Volumes/Lovebox/Applications/SuperDuper!.app/Contents/Resources/Copy Scripts/Exclude Norton FileSaver files.dset
| 12:09:23 PM | Info | Loading 2 commands from copy script /Volumes/Lovebox/Applications/SuperDuper!.app/Contents/Resources/Copy Scripts/Exclude Spotlight search index.dset
| 12:09:23 PM | Info | Loading 0 commands from copy script /Users/kavio/Library/Application Support/SuperDuper!/Copy Scripts/Standard Scripts/Backup - all files.dset
| 12:09:23 PM | Info | /Volumes/Lovebox
| 12:09:26 PM | Info | /Volumes/Lovebox/bin
| 12:09:26 PM | Info | /Volumes/Lovebox/usr
| 12:09:34 PM | Info | /Volumes/Lovebox/.Spotlight-V100
| 12:09:34 PM | Info | Ignoring /Volumes/Lovebox/.Spotlight-V100/_IndexPolicy.plist
| 12:09:34 PM | Info | Ignoring /Volumes/Lovebox/.Spotlight-V100/.store.db
| 12:09:34 PM | Info | Ignoring /Volumes/Lovebox/.Spotlight-V100/_exclusions.plist
| 12:09:34 PM | Info | Ignoring /Volumes/Lovebox/.Spotlight-V100/.journalHistoryLog
| 12:09:34 PM | Info | Ignoring /Volumes/Lovebox/.Spotlight-V100/_rules.plist
| 12:09:34 PM | Info | Ignoring /Volumes/Lovebox/.Spotlight-V100/ContentIndex.db
| 12:09:34 PM | Info | Ignoring /Volumes/Lovebox/.Spotlight-V100/store.db
| 12:09:34 PM | Info | /Volumes/Lovebox/.Trashes
| 12:09:34 PM | Info | /Volumes/Lovebox/Users
| 12:10:21 PM | Info | WARNING: Caught I/O exception(5): Input/output error
| 12:10:21 PM | Info | WARNING: Source: /Volumes/Lovebox/Users/kavio/Pictures/Aperture Library.aplibrary/Jada.approject/AP.Minis, lstat(): 0
| 12:10:21 PM | Info | WARNING: Target: /Volumes/Lovebox Backup 2/Users/kavio/Pictures/Aperture Library.aplibrary/Jada.approject/AP.Minis, lstat(): 0
| 12:10:21 PM | Info | Attempting to copy file using copyfile().
| 12:10:22 PM | Info | Attempting to copy file using ditto.
| 12:10:22 PM | Error | SDCopy: Failed to recover from copy error for file /Volumes/Lovebox/Users/kavio/Pictures/Aperture Library.aplibrary/Jada.approject/AP.Minis: Bad file descriptor
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