Hi. Just tried to do a quick mockup with a situation like yours (glass + object + glass), and I don't have any problem with the alpha channel. I tried both "thin" and refractive glass, and I tried with both plane and boxes as glass panels, but no combination gives me a result like your alpha render.
So there must be something in you scene, materials or setup, that causes this.
I'm using Corona 1,7 by the way.