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I have the very same problem, but with manually started backups.
The problem started for me after upgrading the OS from 9.4.11 to 9.5.3. I have used SD for four years on different successive machines and OSX versions and never had the problem before.
I always do a manually started backup (smart update) at the end of the day of all files on my internal HD, always to the same external FireWire disk, always with the same settings, among which the option to shut down the computer after the backup completes. Sometimes the shutdown occurs as expected, but most of the times the message "Logout has timed out because the application SuperDuper! failed to quit" appears after a while.
I have not been able to figure out if there are specific different circumstances when the shutdown occurs and when in doesn't. However, I noticed that when the shutdown does occur, it takes an unusual long time (much longer than I was used to in previous OS versions) before SD is quit and the machine is shutdown.
If the shutdown does not occur, I can easily quit SD in any way (closing the window, using the application menu, using command-Q) and subsequently shutdown manually. (While writing this, I realized that I did not try a manual shutdown while SD is still running, should try that also.)
Interestingly, when I use the option 'Quit SuperDuper!' instead of 'Shut Down Computer' there is no such problem and SD quits soon after the backup completes.
Intel Core 2 Duo iMac
Mac OS X 10.5.3
SuperDuper! 2.5
(Time Machine Off)
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