Same problem
Am doing a weekly smart update manually to a fire-wire drive on a Macbook (early 2007) running Leopard 10.5.3 with SD 2.5 (v84). Being paranoid, I option to have SD reboot the machine from the backup drive when it is finished, just to be sure I have a boot-able backup.
Recently (2-3 months), it always hangs on shutdown with the message "Logout has timed out because the application SuperDuper! failed to quit". After manually shutting down SD and then the Mac, everything seems fine. But it is annoying. Could this be a OS X problem?
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