I'm sorry to hear that the upgrade to FB4.7 does not fix this problem. I'm seeing the same upper corner of my game pinned to the center of the ADL window. I'm running FB4.6 on a Retina MacBook Pro.
The only solution I've found so far is to make sure the ADL launches on an external display. I attach the external monitor, then move the menubar to the external using the Displays PrefPane.
I'm trying to run debug app in FlashBuilder -- it shows only 1/4 of the app screen in the simulator window. What gives?
Never mind, I switched to IDEA 12 and it works with Air 3.7 just fine. No more bug in adl simulator.
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So, now I tested the issue with newest AIR 126.96.36.1990 –– April 23, 2013 and the problem is gone. :-)
Some words to Adobe Support Team: Your commitment in this case was very small. I hope this will be better in future.