I would bet that the bullet got pulled up when you chambered it and removed it. The bullet sticks in the lands, then when you remove it it gets pulled up. I do it a bit differently now, as I've actually had the same thing happen.
It takes a bit longer, but what I do is seat the bullet deeper and deeper while test chambering it by hand, remove the bolt. When I can just barely feel it sticking in the lands when pushing on the cartridge as hard as I can, but it will fall back out by gravity alone with the barrel vertical, I consider that as .000" off the lands.
Once I have made that determination, I then get an accurate measurement of the seating die from stem to base, then I write that number down for that specific bullet / part number. So when I want to seat that particular bullet say .015" off the lands, I know my seating stem to die base will need to be .015" shorter than the .000" number recorded.
FYI, most, if not all bullets will have some variance at the olgive. With standard grade bullets, the olgive location can vary by as much as .010" or so. Match grade bullets aren't as inconsistent, but they will still have some inconsistency, usually .003" or so.
GS