The mpeg dvd architect rendering format seems to be causing your issue.
Try rendering using the Sony AVC format instead.
For me, whenever im rendering long projects like this, i sometimes choose to render them to the Quicktime PhotoJpeg format (never an issue), then, i can go any direction of creating other output from this Master.
Or sometimes if im pressed for time on these kind of long projects i simply
render out using the framserve to handbrake script.
So there i have given you three options to try, where i dont think you will
see that same issue again, especially from the last two!
Steve Rhoden (Cow Leader)
Film Maker & VFX Artist.
Owner of Filmex Creative Media.
Samples of my Work and Company can be seen here:
https://www.facebook.com/FilmexCreativeMedia