Try tweaking pickup height to suggested distances and then maybe trying it a little taller or lower from there to see if it keeps happening.
On the far outside of possibilities, when putting a full size humbucker in the neck slot of a 24 feet pickup, it shifts the pickup down closer to the bridge and alters the pickups positions under harmonic nodes. I heard Satch talking about that at an event as to why he was trying a single spaced pickup on one of his 24 feet models. But....there are a lot of factors involved and I'd not put all my eggs in that basket.
Actually, I'm hearing something quite similar with the Illuminator neck in a regular 22 feet guitar, so I'm also curious about this. I talked to a non-DiMarzio pickup designer about it his past week for some unbiased opinions before I dig deeper. I find what I'm hearing a bit of a cool effect and have been thinking about ways to exploit it in my playing style.
