OSX appears to cause the application to "hang" if it is minimized for too long or sits in the background too long. It appears the system or AIR framework is placing the application into an idle state. Once you bring the application back to focus, it catches up and works fine. I am able to reproduce this on all version of Adobe AIR. Our application is a real-time application that requires constant connection. We've been able to find a work around where in some instances, simply playing a blank mp3 over and over causes the application to remain active.
I've created a bug case.
https://bugbase.adobe.com/index.cfm?event=bug&id=3746380
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