Andy Engelkemier! Thank you thank you thank you for creating this thread! I had 20+ timelapses with the same resolutions as yours and I had the toughest time getting half of them to export in Media Encoder. I was aiming for H.264, 4K, .mp4 files but I kept getting color bars no matter what I tried (including clearing the cache).
I created a new composition as you did and Media Encoder liked it. I’m finally exporting the rest of my timelapses as we speak. I’ve wasted so much time on trying to figure this out. Thank you for finding and sharing your solution!