After 14 hours of test and re-test, I think it was related to a file that I rendered from AE. It must have somehow gotten corrupted. Not sure how, I didn't get any errors when rendering in AE... I don't know. I give up. Maybe, I'll go buy a Toyota.
After more testing, I found that the files that I rendered from AE are all fine. I was able to add them to a project and save, restart and render.
This leads me to believe that the project got corrupted in the process of editing or when exporting to media encoder. As I mentioned the last time this happened, I feel like there is a bug with media encoder or dynamic link that can on some occasions corrupt a project.
Save early, often and with progressive file names. Hope that helps if you are having this problem.
Glad you solved it and happy editing. These problems are so difficult to troubleshoot, because there is no pattern discernable in how to replicate the problem, so Adobe will often call this a feature instead of a bug.