You are not the first operator to note this problem on this site. It seems not be corelated to any particular rigs. First, we must assume you are playing with your ammo (running through unfired rounds to see this effect). Some folks never see this because they fire every round that is chambered. Also, it would be interesting to see some photos of the gouges in your bullets.
The culprit has at times been the magazine, not the chutes. I assume you find copper gilding residue on the chutes, not the mag.
I also have questions about the effect on accuracy, but with the round spinnng around 200,000 rpm coming out of the barrel, it may be negligible. There can be at least two things involved: 1)asymmetric CG shift radial and lateral, and 2)asymmetric aerodynamics.
I think it would be a good write up for the site to have some bench rest operators take a rat tail file and camera to the range some day with some match FMJ and document the accuracy effect. I am a relatively new member, so this may have been done already.