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Quit LabVIEW (Exit) stops program but doesn't exit

If I create an unsaved vi and drag on the exit icon then run it, LabVIEW tries to close and asks me if i want to save. Correct behavior. However, in the application I am currently developing, the Exit icon just stops program execution but does not make LabVIEW close. I have compared all of my options and preferences between the two applications and can't find A) anything that appears different OR B) anything that even looks like it would cause this to happen. All execution, window appearance and window size options are 100% the same. I really only need this when building an application so it will completely exit and for whatever reason it won't. Any ideas?
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In a built application, you can have your main window open a VI reference to itself and set its own FP.Open property to False. If this is the only open VI, the application will exit. This routine can be wrapped in a Case structure that only executes if Application.Kind is Run Time System.
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