I have your receivers bigger brother so check this first
Go to the Set Up menu
Choose 2. Speaker Setup then 2. Speaker Configuration
If the first item says Subwoofer No change it to Yes
Apologies if you have checked/know this but it's like spending an hour trying to figure why the car will not start only to find there is no petrol in the tank.
Onkyo TX-NR809,Sony KDL50W829 ,Virgin Media V Box HD, WDTV, PS3, Philips DVP9560, Marantz CD67, BK Monolith Plus, KEF TDM 23C,23F & 34DS, Darbee Darblet, Belkin F9G6223uk3M, Buttkicker LFE kit, IsoAcoustics L8R430 and L8R155, Mede8er 800X3D