W-1 Phase, my Yamaha RXV receiver tells me the same from the moment I bought it.
All is wired correctly from receiver to speakers and so on, if I re-wire that single speaker the warning is history. Maybe the internal wiring of some speakers is not correct or the Yamaha has some software problems
I wired all correctly, checked it, played some music and all is fine so the warning I got ain't correct from the first day so I just forgot about that incorrect warning !!
To find out if the internal wiring / phase is fine you could try to use this (W-1) speaker in a 2 channel stereo set up so you can easily hear and find out whether the internal wiring or the phase and external wiring is okay.
If all is fine then do not pay attention to the warning anymore it is just a machine
About the red light on your sub.
-is the sub in the menu activated ? ( on / both ?? )
-play some 5.1 stuff..........