I had a similar problem like the OP's, but with a box of CCI's that were so old the boxes were black and white....probably early sixties vintage and God knows how they were stored before I got them. Seemed like 1 out of every 5 didn't go off.
I learned years ago that a seated primer should be slightly below the cartridge base. If it's even with the base and can't be seated anymore, that's fine also......but in NO case should it be ABOVE the base.
But more on the problem of seating primers. I have two devices that can be used on "suspect" pockets. One is an old Lyman pocket cleaner that looks like a small reamer with a wooden handle. A few twists, tap out the junk and the job is done. On a large batch of brass however, this gets tiring in a hurry so I forked out the dough for a Dillon primer pocket swage. It's a bench mounted tool that uses a cam over center lever to shove a mandrel into the pocket, uniforming its size, and it's very effective.....especially on military brass, as it removed any crimp. But the point is that it UNIFORMS every pocket, ensuring repeatable primer seating.