Did you clone your Melodyne vocal to get a doubled track, or did you re-sing it and then apply Melodyne ?
I get this unwanted "flange" sound when I clone the vocal track, even if I apply random timing and pitch variations (a feature within melodyne editor), it doesn't really go away. However, if I change the notes of the cloned track to make a harmony vocal track, the flanging
mostly disappears. So yeah, it happens when the tracks are identical time-wise, but it's also to do with identical pitch.
I haven't tried your idea of shifting the track by a slight amount, so think I'll play with that a bit, thanks for the tip.