I experienced similar problems while reloading.
I have found a few areas that I believe cause/contribute to the problem:
1st: Using different shell holders. In several popular calibers, I have more than one shell holder. One for the RCBS priming tool and for the press. A couple are not of the same brand. From brand to brand they can differ in dimension. Even on same brand holders, the size can differ. I found this out when using one I purchased over 25 years ago and a new one for the same calibers.
2nd: I have found that not all projectile lengths are identical. So far, this has occurred with Remington bulk in rifle (.284), pistol (.429) and with Speer (.284) and Hornady (.310).
3rd: Be sure that the area of the press where the shell holder sits and the holder is free of dirt and/or powder residue.
4th: Check that the seater die is tightly secured to the press and that the surface area is clean. Also make sure the seater stem is properly secured.
Overall, I have not noticed any effects on accuracy that I would consider a result of any of the above. But then, I'm not a bench rest shooter and have no precision made firearms. I also regularly inspect my cases for fatigue and pressure signs. Again, I've seen nothing out of the ordinary that I would contribute to above.
EDIT 4/13/08: One more area I forgot to mention: Rim thickness. I've noticed a difference in the thickness of the rim on different brands of .303 British brass. I use mostly Remington, but also Winchester and Norma.