With Onkyo you have to go in and assign the audio outputs specifically if I remember correctly from my own Onkyo A/V receiver. it might be a bit different than on the Sony, but YMMV. That's what's not set correctly if I get the gist of what you are saying. Review the user manual on assigning outputs as such. If that doesn't provide a solution, please re-post your exact model numbers for all your equipment involve line by line with your current cable connections. We could try to help from that point. Geek Squad is definitely overpriced 
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-Pedro
Very frustrated! Upgraded to 7.1 Onkyo from Sony 5.1 Niether recievers have HDMI but do have optical. On both recievers, only the surround speaker output is working. I eliminated possiblity speaker or speaker wire problem by taking turns swapping out all speaker connections and they all worked when connected to the surround output of both recievers. The 7.1 Onkyo would also not output from it's surround back jacks but, as with Sony, would only output to the one pair of surround speakers.
I have Direct TV reciever and a Toshiba DVD player that are both connected directly to TV via HDMI. Then from TV, only one optical cable to A/V reciever. We just use input selection of TV to change source.
The only thing I haven't tried yet is to hook directly from satellite reciever and DVD player to A/V reciever versus routing through TV. I have already been into setup menues of satellite reciever and TV to make sure of proper settings. Like I stated previously, I at least made sure that all speakers and speaker wiring does work. Could there be problem with the optical cable? I thought they either worked or didn't. Should I buy a new one?
BTW, I forgot to mention that the powered sub does also work. I just can't figure out problem with center, right & left front, and the surround back speakers (7.1 Onkyo).
I already called Bestbuy and Geeksquad would charge about $140 for service call.
Please help,
Thanks,
Steve
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