For me this problem started a week ago when trying to export from Premiere via queue. I don't remember, when the newest update came out but i am almost sure that i was able to successfully export with the newest version of media encoder at least once.
The problem occurs when exporting to mpeg2 and h.264.
For testing i simply reseted the export job after the goat-sound and started it again. It never fails at the same point twice, but always manages to export a few cuts more than previous attempt. It's almost as if Media Encoder has problems caching the video files it needs.
It's like trying to export directly from Premiere after deleting all cache files and not giving premiere enough time to gather the informations of the used clips. (Try rendering or exporting in Premiere when some clips still say "media pending")