Quoted from other posts in diff forums regarding bolt action vs. semi-auto. Not my own words but some things to consider that may be a possibility.
"It's mostly about repeatability of the firing cycle. A bolt rifle has less moving parts and therefore it is easier to repeat the exact same firing sequence each time.A semi-auto goes through several different motions each time it is fired and each moving part may or may not repeat exactly the same every time."
"also every time a new round is stripped from the mag, small even microscopic grooves, are cut and chattered into the next round down in the mag, from the bolt head and round taken from above, then it goes into the chamber, which if it doens't go in right down the middle, can get little imperfections again, this time on the bullet itself. they may be tiny, but these little imperfections, will cause differing aerodynamics on each successive bullet."
"would the imperfections really be a problem when the bullet enganges the rifling? even then most bolt rifles have magazines to.?"
"Nope. because the curved areas of the bullets especially the tip, and near it, don't engage the rifleing.any little deviation up there is going to effect the trajectory. Imagine if you will , throwing a baseball and a little flap of the cover is not threaded down. Or throwing a football, and the front of the ball, towards the nose , has some of the lacing coming loose. Every bit of this, no matter how small, will change it's trajectory."
"One more factor that has also been pointed out is what happens to the bullet itself during chambering. Manual bolt actions are not nearly as violent in feeding, which means less bullet deformation. A closer-to-perfect bullet means better accuracy. This is why single shot bolt guns tend to be even better-no feed ramp to marr the bullet or distort the case."
With that in mind maybe try different possibly higher quality magazines? Dunno but just maybe it will help some.