Media Encoder Export does not match whats on my PE Sequence

So recently when I sent a project to export from premiere to Media Encoder the exported video file did not match what I edited. For example, I recently worked on a simple photo montage for a client. No transitions, just some simple keyframing. Nothing crazy at all. When I was done I sent it through Media Encoder and in the final export, the images were in a totally different location in the frame. So instead of the photos being in the center, they were located in the lower right area of the screen. BUT if I export it using Premiere there's no issue.  Any ideas what is going on here?