Is the phono section of your Onkyo preamp equipped for a moving magnet cartridge or moving coil? I would be surprised if it was equipped for a moving coil cartridge which you seem to be using. This could be where your problem is. I presume that if you play a CD through the line stage that all is ok which would mean that your problem is in the phono section or with the compatibility of the phono section to your cartridge. Don't forget that the signal of your phono pre runs through your line stage -not the opposite.
Cheers!
Elinor
Cheers!
Elinor