I’ve got the same problem in all 5 of our Intel G5’s running CS3.
This is Adobe’s reply:
Dear Mr. Terrey,
I’ve had a reply from the research team and they have recognized your
issue as a bug (reported in database as (#45802).
They’ve checked the bug details and it looks like they have fixed this
for the next version of After Effects.
The only workaround with the current version of After Effects would be
to duplicate the item in the render queue, after the first render. If
you duplicate the item in the render queue (Apple + D) and then go back
into the output module settings and turn audio on and then render it
again it works. The resulting file will have audio. Only when rendering
it the first time does the problem occur.
Sorry for the inconvenience.
Yours sincerely,
Antoine
Adobe Technical Support