I WOULD RECOMMEND THE FOLLOWING TEST.....
First, what are the primers looking like on the ammo that actually fired??? any pressure signs as in flat primers?
If yes to the above, take a loaded round, place it in the barrel and then "raise" the bottom of the cartridge to get the case past the extractor.
See how far the ammo round sets in the barrel. What I am getting at, is that your ammo MAY be setting too deep in the barrel chamber and as such, the primer may not be getting struck all the time?
Worth a look anyway