H.264 is an 8bit format and the media encoder is not properly dealing with 32bpc, either. It's simply a crap combo. Therefore your only option is to properly render to an intermediate format like a Quicktime file and encode it later. Sure there is some bugs/ several bugs in there, but well...
So I know this sounds really dumb, and thanks for getting back to me, but an intermediate format like Apple Intermediate is what you're talking about? Or is it something else? Under any of the video codecs, and no matter which one I use, it crashes. I can try and try again but I feel like this project will never get rendered and will forever stay on my desktop.
QuickTime with the PNG codec is an excellent intermediate file format.