I had this a few times already now and had to re-render.
In RT and automatic frame buffer output to file sometimes some render elements dont get saved. In my last 5 renders this happened two times. In the past when saving manually I got an error message saying that the render element couldnt get saved. I had to click it and it would go on saving the other ones. Then I would save the ones that wouldnt get saved automatically. Which is more or less fine when you are rendering and saving each one. But with quasi animations I get in trouble. This happens when using RT and the last couple of nightlies between 1st and 10th of May 2017.
Can you send us a sample scene for this issue?