After Effects Renders Out Choppy Video

All of the sudden my project went to rendering out normal looking video to choppy stuff. I have checked all the frame rates and for all of my comps and rendering they are set to 29.97fps.

Also when I preview the render inside after effects it plays perfectly. Even while rendering I can see that it is rendering every frame that I want to. Some how though when I play the quicktime file back it is all choppy. Now it isn't a play back issue I don't think, since it is only a H.264 file and is very small... all the previous renders played back fine.

Now, here is when the problem started. I originally had my comps set to 720p and changed them all to a custom dimension. Changed some elements around, and everything was fine. Rendered a test and previewed fine. Then I went and did some more work on the project and all of the sudden every render is now choppy.

Also now my character that I have a walk sequence on will sometimes disappear... and only if i preview it back in half res will he show up... very weird...

Please help, I cannot figure out what is wrong.

No the issue is not the playback I don't believe. I rendered it out as H.264 and the file size is only 1.4MB. Even in the video I can see that the frame rate is at 29.97fps... really have no clue what the issue is

No neither of those are the issue. I'm not using any footage, all created within after effects. Also open GL is off.

I just tried something weird though and it worked. I created a new composition and put my old comp into it... basically pre-comped my entire project. Rendered it out and playback is perfect.

Seems like a glitch or maybe some file got corrupted somewhere?