I have yet to see two powder measure throw the same weight by volume. Now granted, they can be very close and some times even the same, but take any measure andweigh ten charges and you will have a difference in readings. I think it is just a quirk in the way the powder measure is made or the way you actually fill them or cap them off..

One good point you have is, while a grain or two difference in a rifle may not be important. In a pistol it could make a much bigger difference.