I was still having trouble with the first 11 minutes of the movie ... or minutes 2-11 rather.
Final Cut Pro was refusing to render the PhotoJPEG material .... just constantly stopping rendering. I wound up stopping and starting rendering constantly by hand, so that it would render a little bit at a time.
Eventually it finished, and I tracked down one problem - a bad frame that it simply refused to render. I deleted that frame.
Taking a closer look at the video for this part of the movie though, I realize that it wasn't a good idea to convert it to PhotoJPEG in Quicktime the way I did. The picture is full of scaling artifacts, and doesn't look nearly as clear as the rest of the film.
Since it is running at the correct 24 frames per second, and because it's only 9 minutes of the movie, and because it was so difficult to render, I've decided ... for the time being or just in general .... to leave it the way it is. The opening scenes won't be quite as good quality for those really viewing them carefully. Maybe it's not noticeable, but I notice it.
Hm.
I should have just done the first 11 minutes directly from the M2Vs. Maybe I should have done the whole movie that way. Maybe.