Maya batch render missing alpha channel
I solved my own problem after some more trial and error. For awhile it looked like the fact that I was using Mental Ray shaders combined with general shaders was the problem, but that didn't really make sense so I kept tweaking. It turns out that an image plane I had tied to my camera was the problem. The image on the plane never rendered out, so I assumed the plane wasn't affecting the rendering, but it turns out it was showing up as a black plane when rendered. I deleted the plane for my render and it works fine now.