I can't say if or why that should happen electronically, but I can say that it does happen even with single coil pickups. One factor that might be involved is simply your listening perspective. Since you're inverting phase this happens all the way through the chain to your speaker altering the acoustic interaction between your guitar and amp. Imagine you're facing the amp with you're guitar... Now turn around so you're not, but turn your head so your listening perspective is the same, but your guitars listening perspective is inverted. Sort of like that. It could be that the particular frequencies accentuated by either of your pickups make it more or less apparent. Just thinking out loud.