Ok, so basically I think I am having the same problem. But instead of alpha channeling I was wondering if chroma keying registers into ppt. I am using After Effects on a video to key out the green screen, then trying to input that video onto a ppt slide like this example https://www.youtube.com/watch?v=dgy41dLAqb0.
The PPT program I am using is for PPT X on Mac.
Thanks for the help!