The variances you get in seating depth (base to ogive) are likely caused by variances between individual bullets, even when they're out of the same box. Try measuring the bullets only from base to ogive. You'll see they're not entirely consistent, at least not down to the thousandth. Some bullets types are more consistent than others. For example, I found the 139 Lapua Scenar to be so amazingly consistent (at least within the same lot), that I now only measure the first couple after setting the seater. However, the 143 ELDX can vary .006 or more from bullet to bullet. This is why it's a fools errand to try to seat "right at the lands". You'll never do it consistently.
@Petras - I think you'll want to look into a micrometer seating die. I really enjoy the Redding for my 6.5. When I'm really focusing on precision, I'll back it off a few thousandths, seat the bullet, measure it, adjust the die, and seat it again so that every one measures exactly the same. With a micrometer die, you can do that easily with a twist of the die head.
I started out using the cheap RCBS dies, and if you're reloading for plinking or standard hunting ranges, they're just fine. If you're looking to shoot to 1000 yards or more, consistency is key, in which case, I'd look into Redding or Forester.
And while I'm at it: I'm not sure what your goal is for this ammo, but small groups at 100 yards are great, but may not mean anything at 1000. Your velocity must be consistent as well. For example, you can shoot tiny groups at 100 yards even when your velocity is swinging 100 fps from shot to shot. However, at 1000, you'll only hit when the chambered round happens to line up with the velocity you used to make your dope chart.