Hm ... the problem with stage video (flv) is that it's displayed below the stage3D layer (Starling), and this layer cannot be transparent in the current Flash Player version (it's planned to make that happen, but currently it's not possible).
The problem with embedding the video as a Starling MovieClip is that the textures use up far too much graphics memory -- that won't work, unfortunately.
But if it's an intro animation, you could first display the movie and then start up Starling. That way, you shouldn't run into a problem.