I misunderstood what you were saying in your dock comment. So, Cmd+q issues a direct command, which follows immediately.

But, quit from the dock is different - that issues an Applescript command (It's just how Apple does it). And, our handling of Applescript is different - to prevent a renegade script from quitting the application out from under you, we wait 30 seconds after the UI is idle before we act on a script-quit.

That's why there's a delay there. Totally expected.

Unfortunately 30 seconds is longer than the OS is willing to wait, hence the alerts: You haven't been logged out because the application SuperDuper! failed to quit.

Again, it's 30 seconds past the last active use of the UI. Mine quits fine.