I think you are on the right track that it is breaking in. I would think as the bolt, bolt carrier, and locking lugs wear in slightly the lockup/cycling of all would become more consistent. Also some people think the barrel will break in and smooth out, not sure if I believe that but it is plausible that it could.
My rifle is just over 1 year old and I probably have about the same amount of ammo through mine as yours. When I first got it the gun was very finicky about what loads it would cycle and all were pretty consistent group wise, about .75-1.25" no matter what bullet or powder I was using. Now the rifle cycles consistently but definitely has its preferences. It likes heavier bullets better but not all are equal. The 140 SMK shoots lights out with several loads but the 140 Nosler BTHP will not go under 1". The 139 Lapua with some loads shoots great other times like the Nosler.
The 120/123gr bullets have been a bit of a pain, most groups are about an inch some just under but none like the 140 SMK (1/2"). I just started again with the 100/108gr bullets after your inquiry since I gave up on them when they wouldn't cycle when the gun was new. They cycle great now! I might even have to try the 95gr V-Max again this weekend, I'll be sure to share if I find something worth sharing
Maybe all of that is just coincidence and I just found loads that work better but that doesn't explain why it cycles so much better now with lots of powders/bullets it failed with before.
As for the primer issue, I think it could be several things. I've heard Remington brass is soft and does not hold up well to the near max loads. I would concur as Nosler brass is harder and doesn't show pressure signs as readily as the Remington. Some people have said 5 loads or so is it then the primer pockets get too loose. Do the primers seem too easy to seat when priming?
Also did you see any other pressure signs? My gun ruins the brass if the pressure is too high. I got a popped primer with a load of H4350 behind a 139 Lapua Secenar and a Remington case. I get heavy brass flow into the ejector hole and a mark where the extractor is as well. The charge was .7gr less than the max load listed with a 142 SMK. As I worked up everything seemed fine at 1.2gr under max, then popped a primer .5gr more. Velocity was 2740 FPS, max velocity for sure. But even close to max loads show a little mark where the ejector is.
I checked you're load against the Hodgdon website and they list a max load of 42.0gr of Varget behind a 95gr V-Max. I see the Nosler 6 manual lists 43.0 as the max. Perhaps you are running close to or at max and the brass being used a few times combined to pop a primer. Your velocity seems in line as well. If you have new brass and there are no other pressure signs you may want to try the load again in a new case.
Also is there any copper fouling built up in the barrel? You seem to be shooting great groups so I doubt it but I know this can contribute to a pressure change.
I still like the Remington brass and have lots of it. I just won't run max loads in it anymore unless I am willing to trash it after a few loads. I haven't tried the Lapua brass but everyone seems to like it and say it is very durable. The price is painful though but if I can get a few more max loads out of it then it may be worth the price.
The AR-Comp sounds like a good powder, I may have to pick up a can and try it! I also can't wait to try the new CFE223 powder. I have read rave reviews in several magazines on this stuff. Hodgdon has 2 loads now listed on its website for the 260. They are new as I haven't seen them before and they were not listed in the 2012 annual manual either. They are right up your alley, the 95gr V-Max and 107 SMK
Velocity is 3240 and 3081. I'm sure the other loads will come out soon. Anything that eliminates copper fouling is wonderful!
Find any other loads worth mentioning?