> 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...."
Actually, I think ryck had it right. One boots
from a particular volume or device, and boots
into a particular OS or mode. Check these Google searches to see what I mean:
