If your situation happened after a scheduled backup (or a backup initiated through a custom AppleScript program) failed, it sounds like it could be a known bug caused by the conflicting conditions of SD! wanting to save the current settings, but not 'thinking' it may display UI prompts because of an automated invocation (see threads
3027,
3891, and
4550, among others that reference this bug).
Try saving the settings (Command+S or File > Save). Then all the normal ways of quitting should work again.