I have exported several different files as .mfx's, and everything is fine. However, one sequence insists on rotating vertical. Everything looks fine in the preview before exporting, yet the file that eventually saves is always vertical. Is there any reason why the program is auto-rotating the video? I am completely mystified at this point, because other files of similar lengths, with similar or same video clips aren't producing this issue, so it must be something in the video.
Drag/drop screen-grabs of the sequence settings and the export settings into your reply. If there's something there, we can point it out.
Flying on a hunch:
is it about the first clip in the sequence and how you launched the sequence? Perhaps try a slug of black that has the format parameter you require as the first clip (even jus 12 frames) and put your edited sequence after it.