This is probably the number one explanation of missing audio (or video) segments in YouTube uploads. And if you upload content with multiple audio tracks to YouTube without first flattening the data tracks, all non-primary tracks will be ignored.

Basically, QT X doesn't 'flatten' multiple audio (and/or multiple video) tracks until the data is exported or the merged files are save during the closing pf the QT X app. Therefore, if your Anime export file contains an audio track-even an empty one-and your Garageband output audio file contains one track of audio or the anime file contains no audio but the GarageBand export contains multiple audio tracks or your QT X merge contains multiple audio segments, you could have a problem using QT X to 'mux' your GarageBand-Itunes audio. YouTube is notorious for mishandling uploads containing multiple audio tracks. It could be the fault of all four apps-Anime Studio Debut, GarageBand, QT X, and YouTube. This is very difficult to say since you have not really explained your entire workflow. Is it the anime software or are we doing something wrong with quicktime?

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