That pretty much sums it up. I cut two sequences today. On both of them the GFX were all Ae comps I dragged into Pr. There were full screen, lower thirds, and several that were a vertical third (covered the right third of the frame, while video was running on the left side). Using AME CC to render (from a Pr CC Mac Sequence), the "right thirds" didn't show up either in the renders, or in the compression settings dialog box.
Everything rendered fine when I did it straight from Pr and didn't use the AME app.