I think the exact same thing is happening to me, too. Tried rebooting, nuking the volinfo file and rebooting, repartitioning, you name it.
Code:
| 07:21:48 PM | Info | SuperDuper!, 2.6 (85), path: /Applications/SuperDuper!.app, Mac OS 10.4.11 build 8S2167 (i386)
| 07:21:48 PM | Info | Started on Fri, Aug 28, 2009 at 7:21 PM
| 07:21:48 PM | Info | Source Volume: Luis's Computer, mount: /, device: /dev/disk0s2, media: WDC WD2500BEVS-00UST0, interconnect: Internal SATA, file system: "Journaled HFS+", OS: 10.4.11 (8S2167), capacity: 232.57 GB, used: 209.13 GB, directories: 165732, files: 1116358, ejectable: NO, ACLs: Disabled
| 07:21:48 PM | Info | Target Volume: Backup, mount: /Volumes/Backup, device: /dev/disk1s3, media: Initio WD15EADS-00P8B0, interconnect: (null), file system: "Journaled HFS+", OS: N/A, capacity: 233.02 GB, used: 0.07 GB, directories: 4, files: 7, ejectable: YES, ACLs: Disabled
| 07:21:48 PM | Info | Copy Mode : Smart Update
| 07:21:48 PM | Info | Copy Script : Backup - all files.dset
| 07:21:48 PM | Info | Transcript : BuildTranscript.plist
| 07:21:48 PM | Info | PHASE: 1. Prepare to Copy Files
| 07:21:48 PM | Info | ...ACTION: Preparing Luis's Computer
| 07:21:48 PM | Info | ......COMMAND => Verifying the integrity of volinfo.database
| 07:21:48 PM | Info | volinfo.database OK
| 07:21:48 PM | Info | ......COMMAND => Enabling permissions on Luis's Computer
| 07:21:48 PM | Info | Refreshing Disk Arbitration ...
| 07:21:49 PM | Info | ......COMMAND => Verifying that permissions are enabled for Luis's Computer
| 07:21:51 PM | Info | ...ACTION: Preparing Backup
| 07:21:51 PM | Info | ......COMMAND => Enabling permissions on Backup
| 07:21:51 PM | Info | Refreshing Disk Arbitration ...
| 07:21:52 PM | Info | ......COMMAND => Verifying that permissions are enabled for Backup
| 07:21:52 PM | Info | ......COMMAND => Verifying that Backup ACL support matches Luis's Computer
| 07:21:52 PM | Info | error (5) from /Volumes/Backup. (Input/output error)
| 07:21:52 PM | Error | ****FAILED****: result=1280 errno=22 (Unknown error: 0)
I'm a software developer and confortable with the Unix prompt, so I'm happy to run some commands or diagnostics if it helps.