Media Encoder is moving layer shapes after rendering from After Effects

Hi All, 

I have been doing Holiday videos for 3 years now, in which I project onto object and play a video. I use After Effects to create my solid layers which becomes my template. I then create a 20 + minute video using the solid layers to place the video into so it plays only in that specific location. This is then rendered using Media Encoder. 

This time around for some reason my layers are moving on their own after it is rendered in Media Encoder. As you see in the pictures one is showing the shapes perfectly placed where they should be in After Effects. The second picture shows that the shapes move after it is rendered in Media Encoder. 

The reason I am rendering just the shapes without the video was to troubleshoot the issue, and keep it simple and fast to render, so I left the videos out for now. 

I keep all settings as defaul for the render in Media Encoder. I also included a screenshot of my composition from After Effects which is super basic. Both software are up to date. Any help would be appriciated!