Media Encoder renders incorrectly from After Effects

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?