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I get the "** the application Super Duper failed to quit" message too, when I try to have SuperDuper automatically restart from the backup. I emailed Dave about it some time ago but he was unable to offer a solution. I have since managed to narrow down the problem somewhat, and it only happens when I am cloning to a buss-powered Firewire 400 HDD. It doesn't happen when I clone to a mains powered USB HDD, and it also doesn't happen when I clone from the FW or USB HDD's back to the internal HDD.
I have had this problem since I upgraded to Leopard and through all of its point updates.
Also, after I get rid of the 'logout failed' message, I am able to manually quit SuperDuper.
I hope this helps a little in tracking down the problem.
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