It could be something as simple as a codec issue. Try rendering it out in different ways. It could also be that that section is too much for the computer to handle. I've also seen that before.
Oh! I just now noticed that you said After Effects. I was thinking Premiere was where the issues were. Are you familiar with After Effects or is this your first time using it? A. Make sure you ram preview it not just play. If you just play the video it will be choppy. You have to ram preview it in order to see the clip normal B. If that still doesn't fix your issue then use premiere to render out you video in a different format and try again.
Im somewhat new to it but here, I sent you the video to give you an idea of the problem
Where'd you send the video to? I don't see anything.
through youtube PM