Smart Update running like full erase and copy

[drindiana]

Hi all,
Have been in contact with Dave regarding this issue and although quite helpful he has not been able to offer any specifics to resolve the issue.
I thought I could throw it out there to see if anyone else has had a similar issue.
Problem: Overnight Smart Updates run like the destination drive is empty therefore it completes a full backup which takes hours instead of minutes. If I manually run Smart Update during the day it takes minutes as expected because SD recognises that the drive is not empty. I am trying to figure out why SD thinks the drive is empty. Dave is sure it is not an SD issue but I cannot figure what might be causing the situation.
Any help appreciated.

Logs

First (run manually) completed in minutes

| 11:20:57 AM | Info | SuperDuper!, 2.1.4 (82), path: /Applications/Utilities/Superduper/SuperDuper!.app, Mac OS 10.4.11 build 8S165 (ppc)
| 11:20:57 AM | Info | Started on Wed, Dec 19, 2007 at 11:20 AM
| 11:20:57 AM | Info | Source Volume: Macintosh HD, mount: /, device: /dev/disk0s3, media: SAMSUNG HM160JC, interconnect: Internal ATA, file system: "Journaled HFS+", OS: 10.4.11 (8S165), capacity: 148.93 GB, used: 108.23 GB, directories: 122676, files: 462357, ejectable: NO, ACLs: Disabled
| 11:20:57 AM | Info | Target Volume: Mac Backup, mount: /Volumes/Mac Backup, device: /dev/disk1s10, media: Initio ST3200822A, interconnect: External FireWire, file system: "Journaled HFS+", OS: 10.4.11 (8S165), capacity: 186.17 GB, used: 106.98 GB, directories: 122637, files: 461933, ejectable: NO, ACLs: Disabled

Second (run overnight as per schedule, later than the above)

| 02:30:31 AM | Info | SuperDuper!, 2.1.4 (82), path: /Applications/Utilities/Superduper/SuperDuper!.app, Mac OS 10.4.11 build 8S165 (ppc)
| 02:30:31 AM | Info | Started on Thu, Dec 20, 2007 at 2:30 AM
| 02:30:31 AM | Info | Source Volume: Macintosh HD, mount: /, device: /dev/disk0s3, media: SAMSUNG HM160JC, interconnect: Internal ATA, file system: "Journaled HFS+", OS: 10.4.11 (8S165), capacity: 148.93 GB, used: 108.43 GB, directories: 122679, files: 462425, ejectable: NO, ACLs: Disabled
| 02:30:31 AM | Info | Target Volume: Mac Backup, mount: /Volumes/Mac Backup, device: /dev/disk1s10, media: Initio ST3200822A, interconnect: External FireWire, file system: "Journaled HFS+", OS: N/A, capacity: 186.17 GB, used: 0.34 GB, directories: 3561, files: 12208, ejectable: NO, ACLs: Disabled