Exporting Green Screen as Transparent for Interactive PDF

I am running CS5 Indesign and Premiere Pro CS5
I have a coach on green screen and keyed out the green and have a black background. I am wanting to place the coach only into an Indesign file and have him floating in front of the eventual interactive PDF. I have tried exporting through FLV and enabling the alpha encoder but have not had any luck with it working. Am I missing steps or is there a seperate way to make a background transparent? Thanks!

Todd
I am able to have footage behind my FLV when I import it. I used other footage and even a JPG to double check. The transparency is there it just doesn't export it seems like. I appreciate the help and any other help from other users. I guess the answer is with the interactive PDF and Indesign.

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