Onkyo have Stereo mode, Direct mode and Pure audio mode. All of this modes work as normal stereo mode without activate any other speakers except to Stereo mode that activate only subwoofer with front speakers. Onkyo also have All Channel Stereo mode that activate all speakers in stereo mode.
I have Onkyo HT-R508 past 8 years and I know all of them options and how to work and how to setup.
If him PHONO preamp does not have any malfunction that is all mistakes in him setup.
Audio Technica AT-LP120 USB modded(AT440MLb cartridge),Technics SL-PS770D CD Player,Pioneer CT-S740S Tape Deck,Onkyo HT-R508 Receiver,Mod. Opera Mezza with passive radiator,DALI Trio sub moded with int. amp,HECO center speaker,BOSE surround speker,MDR-DS6500 headphones,M8S media player,DM-800HDse/CS