So apparently Adobe has changed their settings in CC 2014 and Adobe After Effects no longer has the H.264 container, and is only offered as a codec for Qucktime. I've been told I have to go into Adobe Media Encoder for the H.264 codec. That's fine, problem is that Adobe Media Encoder does not really have any options for Alpha. From my understanding you have to set it to 32bpc for it to do alpha in a file, which did not seem to work, but that's irrelevant now because that's not what I need. I need to render out two files for a batch list, one with just RGB files and one with just alpha. I talked to someone from Adobe and they suggested I post here. Let me know if you need details.
Thank you very much.