I’m having trouble with rendering a quicktime movie, and making sure that the alpha channel is created along with it. It seems to just sort of “happen”, all by itself, sometimes, and at other times, not. 
Can anyone provide some guidance on this? I will eventually composite the Blender render with a live-action sequence in After Effects. Many thanks
Ensure the RGBA button is on, not just the RGB
Also, only the Animation codec supports RGBA under quicktime.
My personal experience is that quicktime and blender (on windows) do not work. I always get a 1fps file no matter what settings I set in Blender.