I haven't had to modify my dies or shell holders for my WSM cartridges, but I did have to turn the dies in about a half turn to ensure full sizing due to the press flexing a bit.
It does sound like your press is barely sizing them enough for some cases and not quite enough for others. Try turning the dies in a bit beyond the contact with the shell holder to be sure the press isn't flexing a bit. Measure the deck height of the shell holder as well. It's unusual, but I did have one RCBS 7 mm shell holder that was 0.132" tall rather than the customary 0.125". Before I resort to grinding anything off the shell holder or die, I try using "the companion tool to the press, the feeler gauge
" and put it underneath the head of the case in between that and the shell holder to raise it up just a bit. You can usually stick a 0.005" feeler gauge in there. Then size the case and see if that works. Only then do I resort to grinding something off the shell holder or die.