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The notifications are state transition triggered, so you'll only see a Due Soon or Overdue (or Start) notification when the action/project becomes Due Soon or Overdue (or Available). If it was already Due Soon or Overdue (or Available) when you started up OmniFocus, you won't get a notification. Also, if you don't tell Growl to keep the notifications on the screen, they won't stick around more than a few seconds. I find it very useful to set it to keep them, because if you click on the icon in the notification for the application that sent it, you'll be taken to that application, and in the case of OmniFocus, you'll be taken right to the action, as long as you aren't bitten by a bug involving focused windows.