Kan vara detta som är felet och lösningen:
I'm answering my own question, in case anyone else runs into this problem. Very frustrating until I figured it out.
PROBLEM: Build would always fail, claiming "Muxing Internal Error" in the log.
SOLUTION: In one of my menus, my loop point and end point were set too close together. I had the Loop Point set to 00:00:03:01 and the End to 00:00:03:02. When I changed the Loop Point to 00:00:03:00, the build worked fine, no more error.
One little frame. Go figure.