Those outputs are likely for sending the signal to another amp or pre/pro, but that may not change the fact that the SOURCE may still need to be connected via a stereo analog connection in order for the processor to accept the signal. I am not familiar with the Z9 so I can't say this is the case, but every other unit I have installed has been this way; you could not use zone 2 with a device using a digital input - CD for example - even though using a digital input still means a stereo signal, zone 2 would only function if I connected via the stereo analog to another input.
Have you tried it with any stereo analog sources? I hooked up a system with a music server and we had the same problem - the PC did not have a soundcard that had analog outs, so we got another soundcard that did. Alternative would be a cheap DAC from Radio Shack intended for laptops with optical output that they sell for $4.