Unfortunately I have no ideas but I have exactly the same problem than you. I tried to change some code but I have always a blank flash window.
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Ok it's me again. It works now.The only thing I did is to simplify my FXP (less events on my buttons). I imported it in FB4, converted it in Air project, changed s:Application to s:WindowedApplication and that's all.
Verify that you put a currentState in your windowedapplication.
Thanks for the follow up.
I found that this error is logged as a bug with the development team. My work around was to create a new air app then export my assets from the first app and import them into my new air app. I then copied the "main".mxml text and pasted into my new air app making the designated change from s:Application to s:WindowedApplication and it worked. phew.