What magman said and referred to the bullet comparator.
When I experience the 'problem' you mention it is usually due to the bullets having been formed with nonuniform tips or ogives. When this happens more of the bullet will fit into the seating rod than do others. Thus overall length variance.
I'd really consider the bullet comparator and measure the bearing surface length and sort by that length. Also take the seating die apart and put a bullet into the seating rod and see if the bullet goes in beyond the lead, ie., seating against the jacket not the lead tip.
Or rig up one of these gizmos and drill the holes straight and the correct size for what you want to do and its a pretty handy tool.