I am trying to do a batch render today of a bunch of similar sequences through Media Encoder CS6, but one of my layers is being rendered improperly by Media Encoder. Basically ME is shifting the layer ~10% to the left and then the section on the left that is being cut off is now rendered on the right. Really weird, especially since the actual layer is larger than the canvas and if it was really shifted to the left the right side would not look like this. Rendering straight from after effects is proper, though I would rather not do it this way as CS6 has a bug where often if you switch away from the AE window when rendering it will stop rendering and act as though it has completed the task when it is not finished(bug after bug).
I've attached an image of what ME is giving me, AE output is on the right, glitched ME output on the left. It is the lower third layer below the player's name that is the problem.