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From what I can tell, that's just the way it is. Same thing happens to me with Digital Coax, but the pod has no trouble correctly decoding Digital, DTS, and other signals from the digital out.
I'm guessing it's because the signal sent from the Audigy during the test isn't DTS or Dolby Digital, so the pod doesn't change the mode. If you connect the three analog cables to the Audigy and the pod, choose 6 channel direct and run the test, you'll hear sound from all speakers.
The only downside to not being able to run the test with optical/coax connection is that you can't calibrate your speakers. I've had zero problems with mine, though.
Good luck!
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