Just had a thought while I was playing my Strat - the G polepiece is the tallest one, isn't it?
I wonder if the pickups are too close to the strings? And then, since the neck/bridge and middle pickups have opposite polarity, maybe there's some odd magnetic interference that's only noticeable in the in-between positions. Like "Strat-itis", which is usually due to the neck pickup being too close to the strings and interfering with their vibration.
I know it sounds a bit science fiction.