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https://gyazo.com/559f20774cfeb56ef485ea334026a0df
https://gyazo.com/0f80a2b532200058e252f33308e6081c
This is my first time using after effects so I really have no idea what I'm doing, this is probably an easy fix but I can't find any information online about it. In the first vid you can see I have Clip 1 composition open and the motion tracking is working, but in the second vid where I'm in the "master" composition with music, it becomes very choppy again as if the motion tracking is disabled.
Clip 1 and Clip 2 are edited from the same video and are the only ones with this problem, Clip 3 through 10 don't experience this problem.
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I see playback issues. I see Anchor Point keyframes in the first sample video so it looks like you motion-tracked something. After Effects needs to render a preview before it can playback smoothly. You can open the Info Panel to see when the playback is in real-time.
I'm not sure that I see any tracking errors or problems.
You need to spend a little time in the Learn Workspace and also with the User Guide. After Effects is a lot more complex than an NLE like Premiere Pro, it is not a video editing application, and you should only use After Effects to create shots with effects or graphics or animations that you cannot produce in Premiere Pro or other NLE.
I'm not sure what you are trying to accomplish. A workflow and design explanation would help us help you create the kind of effects or animations you want to create. There is no obvious problem with either screen recording other than a possible playback stutter.