On a similar note, I have an 861 that I use as a per/pro for movies and multi channel music (SACD, DVD-A and Blu-ray). I use outboard amps for L/R (Rotel RB-1572), Shure HTS-50SPA (bridged) for the centre and an amp for the surround speakers.....anyway, I originally had a Rotel RB-1080 amp for the L/R (Mirage OM-6) and after a while found that the surround sounded better with the phase to the surround channels (Ar-9) reversed. A couple years ago, I replaced the 1080 with the 1572 and one day just decided to try the surround speakers now in phase with the fronts and sure enough it now sounded better. I checked the phase with some test disc signals, as I did on the previous trials, but it is sort of hard to hear the differences over wide distances without moving the speakers closer, but it was now better....and I did not think much of it. More recently, I have been listening to more multi channel music including some three channel discs (Nat King Cole). The music sounded great....but there was "something" that wasn't quite right....could not really put my finger on it, but stereo discs had a bit more of a position in the room for voices whereas the 5.1 centre (from the dedicated speaker) was not quite as good!
I checked all the connections, all was good. I tried the "phasing" tests from discs but did not really learn anything. Just on a shot in the dark, I played a mono source through the L and centre speakers ( by reconnecting the patch cords from L/R to L/C) and with my head between the speakers at a crazy angle........the mono sound was diffuse, not centered! I reversed the phase on the centre speaker and low and behold, sharp centered sound between L/C and R/C for the mono signal. All the connections were correct previously, so somewhere along the electrical path, there is a component that reverses the phase relative the the other components.
The sound is now fantastic and sharp for music, with much more presence that sounds "right" vs the great but not quite there from before. Another component change during this time was from a Luxman stereo pre amp to a Rotel RC1580 pre amp that the L/R channels go through on the way to the power amp (stereo music goes through this more "pure" path only), so I do not know exactly when this "change" occurred. The movie sound is now better as well, but the nature of movie sound makes the reversed phase less noticeable than for carefully listened to music.
I do not know if this is helpful, but maybe something is reversing phase.....maybe try the mono listening trial and see what that gives. It can happen!