I had a Savage many years ago that I shot handloads in. It was before I started handloading myself and used my friend's press that was set for his Model 70 Winchester. I had numerous misfires, dispite having a dent in the primer that looked normal. Worse than that, primers were very flat and sometimes fell out. The rifle was sent back to the factory and they replaced the bolt and reset the headspace, but to no avail.
Then, I got my own reloading press and set the dies to neck size only and the problem went away. The other press was sizing the cases too much for my chamber.
In your case, it seems that the headspace could really be the culprit. You should have it checked, or at least try to chamber a fired case in someone else's rifle that doesn't have the problem. If it goes in, the problem is something else, probably related to the firing pin or firing pin spring. If the case doesn't go in, have the headspace checked immediately!!
Picher