So I had a bit of a 'Eureka' moment today.
For the last six months or so I've been getting the occasional light primer strike when using my 9mm M&P, probably averaging about 5% of my rounds and it was only with my reloads from my Lee Pro1000. It was annoying the hell out of me. I'd tried everything, different primers, isolated various case brands, double checked the primers were seated correctly, checked my press was working as it should be, etc. I believed it was my reloads as it never happened with factory ammo.
Well I bought a case gauge this week and think I may have discovered the issue, check out the pics. For whatever reason, about 40% of my reloads look like the rounds in the three rows on the left of the case gauge, the two rows on the right are factory ammo. Once I run them through a resizing die they're fine but I think this may be causing my light prime strike issue. The M&P will fire when the slide isn't quite all the way forward, so if these rounds are causing the slide to sit slightly out of battery, then when the striker fires, it's hitting the round and pushing it forward and some of the striker energy is absorbed by the round moving forward instead of all the energy being put into the primer. Much the same as when you have a primer seated high.
I'm off to the range this week to see if the issue is resolved!