The only difference I can imagine is the way the signal is routed thru the receiver. I called Pioneer CSR a while back and asked if MCACC (room correction eq) was applied to the audio signal received thru hdmi. A few days later they e-mailed me back that the audio signal routed via hdmi went straight to the 6/8 channel anolog inputs which bypass all processing including bass management, bass/treble controls and MCACC (this could be an issue to anyone using the anolog outs of a BlueRay or HD player). I still don't believe them (why would they do such a thing?) but have been unable to verify it. So even though the digital signal is the same, I'd try both to verify the path of hdmi.