360 video sometimes rendering into one flat image

We are rendering a lot of 360 H.264 videos through Media Encoder and usually they come out fine but sometimes they will come out rendered as a single flat image instead of the wrap around image that you can pan around from the centre of. If we just run them through again they usually come out the way we want. Is there some bug or something that's causing this or is there a setting we are missing?

Thanks