Okay another thought occurred to me. You mentioned you bought another set of dies (same brand), did it also come with another shell holder?
If so, and if you have been switching from one holder to the other it is another area where variation can occur (in their depth to the bottom of the die).
If you have two shellholders identify A from B somehow and don't swap them about until you can measure a difference between them .
Homework... look up Redding competition shell holder sets. As GPMac has said don't alter the die or holder by grinding, (if you get it uneven by .002 you have introduced yet another variable)
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