'CoRifleman' - It is not unusual for two rifles in the same caliber to have differences in their chambers and for one with a tighter chamber to not accept a 'fired' cartridge case from the other.

This is usually resolved by full-length resizing.

I would suspect that possibly your F.L. Resizing Die is the culprit.

I just neck-size my brass and have the amazing good fortune that the neck-sized cases will inter-change between eight different Krags!

Easiest solution might be to just keep brass segregated for each of your Krags and try just neck-sizing. (Just loosen your F.L. Die one turn in the press).

If you want to experiment, try switching bolts and see if it makes a difference. (One of your Krags could have slightly tighter 'head-space').

(p.s. Is your 'cut-down' a model 1898 or a model 1896? There was a dimensional change made in the 1898 chambers).