In Flash Builder 4.6 on my MacBook Pro I am created an iPad app. Everything works fine when I compile and test the application. However, when I plug in my dual monitor and run the application it does something very bizzare:
The app displayed seems to have shifted up in it's display window in the ADL (Air Debug Launcher?). So the bottom half of the app is shown at the top of the ADL window, but the bottom of the ADL window is simply the last row of pixel repeated all the way down. In order to interact with the elements on the screen you have to click where they would be if it was displayed right, not where they actually are being shown in the ADL window.
I have found that if you drag it to the laptop screen and leave it there, it will act normally randomly on it's own or when you click it. Sometimes it will do the above shift but will snap back if you click somewhere in the window again. But only on the laptop screen. It is pretty much unusable on the external monitor.