That's what confuse me. Unless the neck thickness varies widely which I doubt, then the only other two things that could vary between pieces would be springback rates, or the uneven application of that oxide layer from annealing...
The forces you're feeling on seating come from three things:
1) The amount of material being expanded combined with the ability of that material to resist expansion (spring back).
2) The coefficient of friction between the bullet surface and the neck surface.
3) The bearing surface area - this obviously grows as you seat, at least until the beginning of the boat tail clears the neck, at which point it remains constant.
So, here's where you can get some issues:
1) You've got inconsistent spring back:
a) Due to inconsistent neck thickness, which causes differing amounts of spring back
b) Due to amount of material expanded due to inconsistent inside neck diameter
c) Due to inconsistent inside neck diameter due to too much carbon build up in the neck (unlikely)
2) You've got inconsistent friction:
a) Due to varying amounts of carbon from one neck to another
b) Due to different surface conditions from one neck to another
c) Due to inconsistent application of graphite - which could be exacerbated by annealing
d) Due to varying surface conditions of the bullet (e.g. you pulled a bunch and they get marred)
3) You've got inconsistent bearing surface:
a) Due to varying length of the flat area of bullets - see previous post and the orange plot
b) Due to varying neck length
I'm sure I missed a few things, but these are where I'd start to try and narrow down what's causing the issue. And get the force gauge fixed. Getting decent data is key here - it might be (probably is) a few of these things, and simply guessing at how much each one helps is just going to cause frustration.