It is a long-shot that this will be of any help, but I had a similar problem a while back trying to import a flash movie with transparent BG into a PDF. Turns out I had to have the latest version of Acrobat - no other fix. Read this short thread, might give some food for thought:
http://www.experts-exchange.com/Software/Photos_Graphics/Web_Graphics/Macromedia_Flash/Q_24448012.htmlgood luck!