Reidy reported that some primers were flush with the case head while others were below flush. As some of us, handloaders, have sadly found out; primers that are not fully seated sometimes fail to fire. We believe this is caused by the firing pin expended seating the primer rather than crushing the priming pellet. I suggest he try firing the misfired cartridge a second time. If it (they)had the primer seated by the first strike, the second strike may fire it. I'm not suggesting this for regular usage but for diagnosis.
Mike