> When I make my clone I reboot from the drive that has the system and Super Duper, and I instruct SD to make a clone of my main drive onto the partition reserved for it.

You slipped... You "reboot from into the drive that has the system and Super Duper...."

The new Great Equalizer is the SEND button.

In Memory of Harv: Those who can make you believe absurdities can make you commit atrocities. ~Voltaire