One reason you may notice a difference between the six channel analog input and the stereo bypass mode... a difference in bass management. Do you have a subwoofer, and do you have your mains set to large in the 950's setup? If you have the mains set to large, the sub will get no signal using stereo bypass (when set to small with stereo bypass, the mains get the unchanged analog signal, but a copy of the signal is converted to digital and run through the bass management to generate a subwoofer signal). On the other hand, with the six-channel analog input, a low-pass filter always produces a low frequency signal for the subwoofer, even if the analog bass management is off and the mains are getting an unfiltered signal (the "double bass" condition that was heavily debated when the 950 came out).

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