The seating die is probably contacting the bullet at a different spot along the ogive. See if you can adjust the seating die to replicate the length you measure with your comparator. (Don't worry bout the specific number you need to dial into the micrometer die. )Then see if that measurement is repeatable. (in other words, if you always seat using measurement x on the micrometer seating die, it always measures Y with your calipers and the comparator). If the bullets are consistent, hopefully, you should be able to make a direct correlation.