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Rendering with an audio codec selected will cause problems
Rendering with an audio codec selected and mixdown unchecked, will result in dropouts in the audio track.
Rendering with an audio codec selected(ex. mp4, h.264, ac3) and mixdown checked, will result in dropouts in the audio track.
Rendering AVI JPEG and mixdown checked, will result in dropouts in the audio track.
So, maybe it is necessary to do something like this to overwrite the audio when mixdown is checked? Or even strip the audio from the rendered file and then mux the mixdown audio in? https://superuser.com/questions/602662/how-do-i-replace-the-audio-in-an-mp4-file-without-re-encoding
If no audio codec is selected, there are no dropouts in the audio.