out of phase usually mean the wiring of the + and - (Hot and ground) on one pickup is in reverse with the + and - of the other pickup.
one pickup alone, cannot be out of phase with itself.
Unless you have changed the wiring connection internally of the hot and ground wire of one pickup relative to the other pickup and in the middle position of the pickup selector switch(bridge and neck pickup in parallel) then you will get out of phase.
if not, most likely the unique sound could come from the change of postion of the pole piece(on the pickup) in relative to the strings. With the changed position, the pole pieces are picking up the strings vibration slightly further away from the neck, thus having that sound you are hearing.
anyway, just my guess for the sound taht you are hearing, so do take it with pinch of salt.