I have further experimented by doing the same with a Yamaha AW4416 and to my surprize I hear the same effect. I must say I am using as a sound source the Yamaha TX81Z FM synth LatelyBass preset in an arppegio loop. The signal is unbalanced but I wouldn't know immediately how that would effect the situation if it were a balanced signal, really.
On the Yamaha AW4432 you can route the exact same signal to multiple channels which the DDX cannot do. That way, by inverting the phase of one channel, I could check if both cancel each other in the mix and yes they do. This means this is proof both signals only differ in phase and nothing else.
So it seams with low frequencies a phase inversion can be recognised by hearing as absolutely different, this means not only at the moment of phase switching or in reference to an simultaneously sounding non-inverted signal.
If anyone can explain the physiology of this just go ahead.