Audio missing when shared to QT

Hi,
I've shared a 52minute movie original in iM6HD to QuickTime and on two occasions the audio is completely missing in the resulting .mov (and also a .wmv version I made).
This is a pain as it takes hours to save to QT.
Where am I going wrong, guys?
TT

Your audio settings may have been changed.
1. Open Audio MIDI Setup (/Applications/Utilities/), then check the Audio Output setting.
2. Change the Audio Output setting to 44100.0 Hz.
3. Quit Audio MIDI Setup.
More info here:
http://support.apple.com/kb/HT2178?viewlocale=en_US
More info on audio missing in iMovie here:
http://support.apple.com/kb/TS2289
Alternatively, if the audio was from copy-protected tracks from iTunes, they won't copy over. If that is the case post back for a workaround.

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