I had the same problem with one of my target rifles, took the bolt apart completely, and cleaned thoroughly.
Put it back together again and used the misfired ammo in it- BANG!
Some of the primers had deep dents on them, but the firing pin was hitting them too slowly.
had the same issue with a '996 Mauser years ago, as well.
Cat
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Anytime I figure I've got this long range thing figured out, I just strap into the sling and irons and remind myself that I don't! 
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