I really appreciate your ideas! I have already tried:
1. reset the preferences
2. I did try to encode a success file from last year which is half the size of the current project with the same “not entire movie” result
3. plenty of drive space with no RAM issues that I can see
4. tried to encode the project on a dinosaur MacPro machine from 2006 using Lion and Compressor 3 with the same “not entire movie result”
Could this be a Quicktime issue?