I've always considered flattened primers to be a sign of approching max pressure. That's what I was taught many years ago, and I've stuck with that since.
If you're close to max w/ virgin brass, and that brass hasn't "swelled" to form to you're chamber dimensions; then you're probably gonna see more pressure signs once the brass is fireformed a little (pressure has less room or space to go before the bullet starts moving). Also, if you got enough case stretch out of one fireing/re-loading; then the necks could be just long enough to be pinching the bullet before release, which would cause more pressure.
Just some ideas, can't say for sure that either one is the case, but when you said flattened primers that was my first thought.
I used to load a 220 Swift to the point of flattened primers and then had to FL size every fireing. This caused enough case stretch that I was trimming the necks every other fireing. I finally had some brass come apart in the chamber (case head separation due to excessive headspace and constant standard FL sizing)
talk about ruin a hunting trip!! Didn't have a cleaning rod/brush or anything to remove the brass that was stuck in the chamber and had to go home early.
All it took to remove it was a .270 bore brush shoved up inside just past the neck and then pull it back out, but when you don't have it with you.........??
After that experience, I started using neck sizing dies, didn't load quite so hot, and when I FL sized; I didn't do it any more than absolutely necessary. Had many many years of trouble free shooting from that gun thereafter. Got better accuracy w/ the somewhat reduced loads too!