I had the same problem with my Ruger M77 RS in .35 Whelen and the reloads I was making. I couldnt figure out why I had so many misfires until I went onto a forum and asked this same question. What I found out was like a lunk head, I wasnt running the brass through the full length die before reloading the brass. I looked at the unfired, new brass and the shoulder was rounded instead of the nice sharp angle it is suppose to have. So I started full length sizing the brass and havent had a misfire since. I looked at some of the Remington ammo I still had on hand and the shoulder was rounded a bit as well, not as round as a brand new piece of brass, but maybe it is just round enough that it wont fit all the way into the chamber without some sluff in it. When the pin hits the primer there is just enough give to move the round forward a bit. I also seat the bullet so it is only about 3 mils off the lands and it really helped with the accuracy. My Ruger shot all the Remington ammo I ran through it and have never had one problem with any Remington ammo I used prior to reloading.
Good Luck
Chief