When is a Clone not a clone?
 

I had a minor problem the other day, so I booted from my firewire clone, which I have set to erase and copy three times a week. I noticed that it is not a copy of my HD. For one thing, I had 38 apps which needed updating, as per Versiontracker, whereas I only had 3 on my HD. I also had a couple of programs which I had "turned off" on my HD, which were very much alive on the clone. If Superduper is supposed to wipe the clone and copy over everything on my HD, why is it not identical?

It's very hard to know, but I'd guess that your schedule isn't running because your Mac might be asleep. Did you check your logs to see when your last backup took place?

When is a Clone not a Clone?
 

It is running on schedule. I have checked the logs.

Then I can't think of any reason why things wouldn't be updated as expected. We've never seen SD! not copy things it should. It's possible that VersionTracker Pro is misidentifying things, and that your "turned off" programs (not quite sure what you mean) are sensitive to the volume name and/or device.

Could you send the schedule logs into support with the "Send to shirt pocket" button?

Done. On its way to you.:)