Thanks for your response Kevin. You are correct in the 2 ch bypass mode, if mains are set to large, no sub and if mains are set to small you get 80hz xover and sub.

On my system I have the mains set to small and the sound between the digital inputs and the 2ch analog bypass is so close I can't determine which is better sounding. But when I experimented with the 5.1 analog inputs (just using main l/r inputs) the bass became boomy and the overall sound was inferior in my judgement. Could this have something to do with the phase issue?