for me this phenomenon is nothing new, real amps do it, too.
That´s why strumming open position chords with a hi gain amp sounds bad (remember Smashing Pumpkins? ). the complexity of interval relationships always creates a more or less odd clash of frequencies. fifth intervals, i.e. powerchords, have a simple frequency relationship. that´s why they function well with distortion. play a high third with any heavy distorted amp and listen closely, what strange out of tune low notes appear.
Add the compression you get with distortion and you have plenty of frequencies extremly amplified, fighting against each other.
try this:
-play a high sustained E und adiddionally a chugging muted rhythym on the low E string
-then play a high sustained F und adiddionally a chugging muted rhythym on the low E string
-compare the results, it´s octave against minor second
PS:
be sure to try all those things with a real amp, too!!!