Another possibility is maybe the preferences some how got corrupted. That's always been a problem, something that just happens sometimes. You could try deleting your poser prefs and then restarting Poser to see if that resolves whatever problem you're having but I have both P9 and Pro 2012 on my system and they export PNG's exactly the same.

 

I should mention I've tried it both with the background shader and with the background color and it still exported with transparency.