cruel1079 said:

Remuxing didn't work and it doesn't play in Quicktime, but that it isn't an issue since it mainly needs to go into after effects. I did try using Handbrake but I didn't want to lose quality, but I will try using your settings thanks.

Sorry to hear that. Have you tried downloading Perian? It's basically a swiss army knife Quicktime plugin that plays a LOT of audio/video formats. Unfortunately, it's no longer updated, but I've had good luck with it over the years.

I had another idea, which is to convert the footage into Apple's ProRes using Hybrid or another program. ProRes is practically lossless, but with much smaller file sizes. It's also designed to work well with editing software, unlike h.264 which is really more of a delivery format (i.e. good for watching). The only issue is that the ProRes files will be much bigger than x264. But I think it's worth it.

Sorry I didn't tell you about ProRes before. It totally slipped my mind. :(

Anyways, I hope this helps. :)