The problem lies with the mov file format, and the conversion process within YouTube when a video file is uploaded. This can be overcome by converting the mov file to a specific format before uploading. MP4 video and AAC audio seems to be a reliable combination.
YouTube's file format and editing tips for Apple users gives details.
How to convert
First, open the mov file in iMovie (begin a new project, import the mov file as a clip, then add the clip to the project).
Enter a file name to save as, and choose a location to save to. Then click the Options button to specify the file format.
Click Settings for video and choose MPEG-4 Video as the compression type.
Click Settings for audio and choose AAC as the format.
Confirm all changes with the OK button, then wait for the finished mov file to be produced. Upload this file to YouTube using the YouTube website upload tools.