Thanks Dave,
After rendering with every quicktime codec in the list and making notes on quality & file size, I ended up having to use the animation codec (with one and a half minutes coming in at 6 Gb) and then visualhub to compress them to mp4 for editing (like you said). If anyone else knows a better way, I’d love to hear it. Seems to be a major shortcoming with AE which is otherwise a brilliant package.
R