Warning:

At the least, I would test some of your pistol primers, by 'firing' in otherwise empty cartridge cases, to make sure your Krag's firing pin does not penetrate the thinner cup of the pistol primers.

For good reason, there are pistol primers and there are rifle primers. They are different, especially, in regard to strength of metal 'cup'.
Most rifle firing-pins strike harder than pistol firing-pins. Also, the Krag rifle cartridge will develop 2 to 4 times the pressure of some pistol cartridges.

IMHO - Something is wrong.

Maybe the 'Western 29' cases had their primers 'crimped' in place.

Many U. S. military rifle cartridge cases utilized a primer crimp. This needs to be removed from the primer-pocket in order to seat a 'fresh' Large-Rifle Primer.
This is done with, (either swagging or cutting), primer pocket tools.

(A couple of primer-pocket tools that will remove 'crimp' - cost about $14 online):

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