I would look at the bedding and redo. Even if there is bedding under the action, it may not have been done properly and not actually touching the action. Try loosening the action screws and see if the action springs back. Also check to see that the action screws have not been he-man tightened. Firm hand pressure is all that is needed.
Are the bullets touching the lands? Can you get a chamber cast made? What type of powder are you using? Primer? Try shooting over a chronie.
your gear sounds top drawer and should not be causing these flyers. Check the volume of the brass to ensure that there isn't a few that is overly large or small. Just pour in some very fine powder like H870- tap the case to settle and then dump into the next one. If the volumes are the same, the powder will settle very nicely at the top of the neck. Haven't found a problem with my factory brass yet.
Finally, do you have a scope with a proven track record. Sometimes even the best fail internally. Ensure that all mounts are nice, tight and straight.
Have you tried shooting the rifle without the muzzle brake
. Not pleasant but if the brake is not concentric with the bore, will cause flyers. Also check the diameter of the "muzzle" on the brake. The bullet should not touch the sides/bore.
I have had a brake that was so tightly machined that you could see traces of copper on the edges of the brake. Good thing this one was on straight. A little opening up and voila, end of problem.