I had marked the bullet with a sharpie to see if there were any marks on it. I ejected the shell to look at it and while I didn't see any marks in the bullets, the bullet was pushed in the case quite a bit.
If you didn't see engaving marks (and I didn't see any in your pictures), you never hit the rifling.
Rifling marks are unmistakable.
That said, Hornadys have an awfully short ogive radius that might hide classic rifling marks.
Lets look at other issues:
First: Have you tried to chamber multiple empty/resized cases to make sure the cases chamber easily, and the only variable is the bullet being introduced into the equation?
Second: Forget the OAL in the manual.
Third:
Forget the "bullet in the case/close the bolt" method to determine OAL.
Fourth: At a minimum, use the cleaning rod method to determine true distance-to-lands for
your rifle.
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Cleaning Rod Method:
Gently push a bare bullet into the chamber and up against the rifling using a wooden dowel. Use a cleaning rod from the muzzle to slightly push the bullet back & forth on-again/off-gain from the rifling against the dowel. when satisfied that the bullet is just barely contacting the rifling, mark the cleaning rod w/ a razor blade right at the muzzle.
A good starting point for OAL is then an assembled cartridge 20-30 thousandths shorter than that -- i.e, the cleaning rod will sink deeper into the barrel by the diameter of a small paperclip before the bullet stops it.
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Out of curiosity, what rifle is causing this problem?