Your post only just now turned up for approval for some weird reason – I see it is many days since you submitted this. I am truly sorry that it took this long. I have no idea what happened.
But to your question! Yeah, as a work-around you could export as mov or a sequence of png’s and use iMovie to convert to mp4 (if that is the format you need it to be in). However, it is of course not meant to do that – it aught to just work without the glitches exporting directly as mp4 from AP. Would you mind sending me your .ap file, so I can try it here and see if I get the same problem? If I do then this will help a lot when we hunt for and fix the issue.
My email is the one you got your activation key from.
Thank you! And once again, very sorry for the delay!