Are you using the .png file in an advanced template? The advanced templates take the images and convert them to Flash for the interactivity (or in the case of the iPad versions HTML5) and unfortunately you lose transparency that comes with .png files. A work around is to make the background of the image to match the background color of the theme (Try to avoid gradient theme backgrounds when you know you’ll be using images within the advanced screens).
In any of the basic screens the Authoring Tool will maintain transparency with .png images.