This may not apply here, but I had a similar problem with my Father-in-Law's rifle. The gun was a Model 70 Stainless Classic in 300 WSM
. It never really shot well. Groups averaged 1.5-2" on a good day. Sometimes much worse. He sent it home with me because I needed a project and this sounded like the perfect one.
After shimming the action with washers to float the barrel, and adjusting the 4.5+ trigger the gun shot 1-1.5" groups pretty consitantly. From there I started working on handloads. After resizing 100 once fired cases from this gun and making up various loads to test I decided to run a few through the magazine just to make sure they'd function.
The first round went just fine. The second round wouldn't chamber. The third round chambered but only with a fair amount of force. I checked my overall lenth to make sure I wasn't jamming the bullet into the rifling, but that wasn't the case. Then I tried a factory round and it chambered just fine. I scrubbed the chamber and that didn't help. Now I was confused.
I took an empty full length sized case and tried that. I chambered fine. When I tried to chamber the same case again, it wouldn't go. I tried again and it wouldn't go. Tried a third time and it chambered, but it was pretty tight. Now I was really stumped. I took a marker and put a reference mark on the case. Then I tried to chamber it with the mark on top. The round didn't chamber. I then rotated the case .25 a turn and tried again. I continued this and after rotating the case 270 degrees, it chambered fine. I tried it again and again with the witness mark in the same spot and it worked every time. If I rotated the case though it wouldn't work.
Now that I knew that there was a chamber problem I took a look at the once fired brass. When I rolled them on a flat surface, they had a noticeable bulge on one side. To fix this, I trimmed .005 off of the shell holder and resized the cases a little at a time until the die was adjusted to size the case down enough to chamber. Then I had to pull all of the rounds that I loaded, resize, and reload them.
In the end it was worth it. The rifle ended up shooting groups in the .75-1" range with anything I tried. Especially the 168 TTSX which would occasinaly shoot slightly better than .75. I destroyed every case after it had been fired twice. I just wasn't comfortable loading the cases multiple times having bumped the shoulder back like I did. Unfortunately my Fater-in-law decided that the rifle was damaged goods and traded it off for a SRH 454.