Try and chamber the modified case to make sure it fits in your chamber.

There is always a possibility your freebore diameter is tight, thus not allowing you to push the bullet all the way to the lands.

If your measurements are correct, this means the factory round would be jamming the bullet into the rifling, making it hard to extract a live round.... Most likely pulling the bullet out of the case and spilling powder all inside the chamber and receiver during extraction.
If it's hard to close the action on a factory round then it's most likely because the bullet is being jammed into the rifling.
And if that's the case, you wold have to send the rifle back to Savage to have it corrected.