Super Duper Damages Shared Components

After losing a hard drive on my 1.67 gh Pbook w 2 gigs ram, running 10.4.11 I'm using Super Duper to back-up the drive. I've created a bootable back-up on a FW800 external drive. Everytime I use Super Duper to back-up the drive, it damages Photoshop CS3 which won't launch. I have to re-install and it tells me it's currently repairing shared components. No other apps have problems after a backup, and I don't have any Pshop problem until I backup. I tried using Carbon Copy Cloner and got the same results, so it doesn't appear to be the backup app. The thing that's most confusing to me is why Pshop would be messed up on the laptop's HD, which was being duped?
Any ideas?

I've been using Superduper to clone my main drive to do testing and have had absolutely no problems with SD at all. And I've been doing this all summer. so its not the software.

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