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answers:

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As an example, this can be observed if a progress indicator is running and main menu is pulled down. What is the best way to avoid this?

+1  A: 

Originally, apps did continue while menus were open. It was changed later in OS X's history — I want to say 10.3. The reason things appear to "stop" is that, when a menu is open, the app runs in NSEventTrackingRunLoopMode. So run loop sources have to be added for that mode if you want them to continue when a menu is open.

Chuck