It turns out the occasional moving diagonal lines on render I posted about earlier, don't happen if I render in smaller chunks in H264. FYI anyone who runs into them.
But for some reason when I render in chunks, they work fine, but on reimporting them to render all the chunks together, each chunk reimported changes size and I have to resize them to get them back to normal. And I am a bit worried the picture is changed during this resize process. Any guesses on how to get them to not go from 100% to like 133% size when I reimport them..