Assuming similar muzzle velocities and bullet weights... it might have something to do with the powder used and how complete of a burn that powder has during it's time in the barrel. In other words, what the pressure curve is relative to barrel length... where it "peaks" and at what point before the bullet exits the barrel.
Or... it could just be how fatigued you were when you fired the various loads.
That's all I got.... I'm interested in what others may have to say about this as well.
Cheers,
C