Ahhh, sorry for my confusion. Let me see if I've got this now. Your MB is outputting digital audio over optical (verified by using the Z-5500), and your Onkyo is set up correctly to use the optical input for the PC source selection and it works (verified by using the TV). Correct?
If so, it seems like an issue with the format being output by the MB compared to what the Onkyo can interpret. You can check the format in the MB's "Audio MIDI Setup" panel (and maybe other places).
EDIT: Either that or, and as you mentioned, the signal is too weak for the Onkyo. That's what I meant by hooking the MB up to the TV's cable, because I'm assuming that it's shorter - and you might be able to verify if it's the cable length causing the issue.