From your layers, I don't see the problem. And I can create the background video playing through the transparency. I suspect your video, but have no idea.
A test: from the Encore library, General set, add the "Crib Menu HD" (doesn't matter whether your project is hd or not.) Take the "Baby Room Motion Menu.m2v" and use it in place of your motion video asset. (I cannot tell from the screenshots what you have there.)
Render. Any difference?