I just rotoscoped out a pylon from the background a shot using a motion tracked still for fill. It renders fine directly from After Effects, but when sent to Media Encoder for rendering, the motion tracking isn't working. Please see the two renders (fill on left side of 2nd shot) for comparison.
Good After Effects render: https://www.dropbox.com/s/rk3kkopliewdfym/AE_Render.mp4?dl=0
Bad Media Encoder render: https://www.dropbox.com/s/4k5y2rbrmwk21y7/MediaEncoder_Render.mp4?dl=0
What's going on? Help?
It's easiest to see if you go frame-by-frame. Motion tracked area is just below the phone and coffee.
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When something like this happens, it's usually quickest to just drop the After Effects render into the Media Encoder Queue tab and use that instead.