If the 5.1 channel is a bypass of all the digital domain set up on the 950. Why would setting the speakers on the player affect the phase. Or is it the case that the speaker/system configuration of the 950 is applied to the 5.1 channel input?

Kevin may be able to answer this better than I can, but I believe the problem lies in the 950's analog bass management being applied to a signal in which some channels have had differing delays applied to them by the source -- so when those "staggered" signals are passed through the analog filters and the low pass info from them combined with the LFE, the low pass information is also "staggered."

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