Dropped Audio Tracks

When I export a sequence using the "Export QuickTime Movie" (no conversion) I sometimes lose audio at random points.
It happens sometimes when it's an additional track beyond the first two, but then sometimes it will drop the first two tracks also.
As a result I have to use the conversion, but it takes longer.
What am I doing wrong?

Sequence>Render Only>Mixdown. I know it was there in FCP 3, so it should still be there.
Sorry for not being specific in my first answer.
Shane

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