Turn on multiplexing in your settings. You have encoded as elementary streams, which causes two files to be generated.
But the thing is, I edited the video at a Film School and due to their tough schedule I can't go back. But I have the files on my computer. So, is there a way to make the files I have into one file? Obviously I can't encode the project again.
Again thanks for your answer, but unfortunately I can't try your solution.
Have a look here: http://search.wareseeker.com/elementary-stream/
and more specifically: http://wareseeker.com/Video/imagompeg-muxer-1.1.zip/355481
Also when you Google for "Multiplexing elementary streams" you may find additional solutions.
Thank you so much! Very helpful.