Well, I'll go ahead and reply to a two year old unanswered question :D

Damfino why it does this. But I'm glad to finally know *when* it does it.
Until your post I hadn't noticed the connection with quitting with the
window partially off screen. All I knew was that once in a while the window
would appear too cut off!

My fix for it is to open the file with a plain old text editor (TextEdit,
TextWrangler, etc.) and "save as", replacing the original file. Of course
you'll lose a bunch of render settings, but at least now you'll be able to
actually reset them.

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