I found that, if you have show up as muted in the mixer and save the file that way, (on tracks that you've setup with Mutes in the bar settings), they sometimes don't unmute while rendering. This appears to be a bug.

Also, if you have Mutes in the bar settings, that leave instruments muted at the end of a song... when you render the song, those tracks remain muted in the mixer. Then if you save the file (with those tracks muted), you run into the problem I described above. Or, at least I have.