Add me to the group that thinks excessive headspace might be the issue here. The gauges mentioned will tell you if your chamber is 'standard' and that is a good reference for shooting factory ammo. Custom rifles can vary in chambering, yours might be at the maximum end of allowable length while you are full length sizing the fired brass down to minimum. We'd like to believe that everything is always 'right on the numbers' but that doesn't happen too often. I have 4 .308 Winchester chambered rifles, they all get ammo sized with the same die, BUT I have a set of 'die shims' and each rifle uses a different shim to be sized 'enough' without pushing the shoulder back as Mark talks about in his reply. Yes, that means that the ammo does not easily interchange between the rifles but they are used for different purposes and having the brass fitted to the individual rifle is worth it to me.
Bruce