Clinkerclint, need photo's of the rig, and walk me through the builds.

Hence was the upper receiver barrel socket trued?
Was the barrel ramps polished, made sure that the receiver extension type ramps match the upper receiver in play, and even copper solvent cleaned the barrel before it was installed and then again before it was shot?
When the barrel was installed, was it tight in the upper receiver socket or did you have to loctite in in place?
When the barrel nut was tightened, tightened first to 30ftlbs, loosened, tightened again, loosened then tightened to 35ftlgs, then torqued more (not to exceed 80ft lbs) to index the barrel nut channel for the gas tube to the upper receiver.
Did you check the gas tube index with the carrier and key (without the bolt) to make sure they where aligned?

Ditto on walking me through the lower receiver build as well (what parts where polished, cleaned up before they where installed.



Lastly, have you single shot sleed'd the rounds to confirm that the bullets where not getting cocked on feeding in the cases.   What distance has you set bullet jump to off the lands, and regarding the loads, are you trying to use long range loads that may take more than 100 yards to sleep, on short distance targets isntead?

To add, since it sounds like both barrels are production barrels (not hand lapped barrels), have you shot the barrels enough to both stress relieve them, and to allow the bullets to lap the barrels isntead.  Hence on a production barrel, it may take up to 300 rounds before the barrel settles in instead.

That's the glitch, since on a button rifled barrel, you need to let the barrel stress relieve to begin with, then let the rifling fire self lap next.

I'm not saying that you have too let the barrel glow, but you do need to get it hot with some shot string instead. So watch your shot strings (20 round counts), and don't get the barrel all copper fouled up until it does have a chance to both stress relieve and unify the rifling.

Also to point out, shot strings in the 10 to 20 rounds, and not the two's and few's shots instead.
It's an auto loader, and you want to see how the rifling is doing with fouling during the longer shot strings to not foul out quickly to open the group instead.

Here is the Glitch, boat tale bullets do not want to jump to lands more than about .008" to the lands on ignition.




So from the start, you need to figure out the OAL of  any given type bullet in the load is going to be for a Zero jump to lands OAL.

There is a few ways to do this, either with a stoner OAL gauge, or just smoking a dummy round bullet with dry loadings, so the first thing you need to do is figure out what the OAL of the round with a specific bullet (will change as you change bullet types) is to begin with for a Zero jump to lands.  

Once you have this figured out, then step two is to see if a few dummy rounds loaded .004" shorter OAL is going to fit into a mag and function out of it.   If they will not due to being too long, then to use such, you will need to single round Sled the rounds in instead.  
To add, when you are messuring OAL of the round, use a ogive gauge, and not just to the tip of the long ogive bullet instead.


Now back to bullet jump, and as stated, if you are coming out of a mag, and can not get the OAL of the round with a given bullet so you are less than a .008" jump to lands, Then a Boat tail design bullet is not the ticket.  Hence the long jump end up with the engagement of the bullet to throat uneven; so less accurate to begin with, and even longer for a bullet to sleep as well.  And not uncommon for a long range load to group at plus MOA at short distance, then to go sub MOA at the the longer distance instead.  Hence until the bullet sleeps/goes perfect spiral, it is moving down range in a small circle pattern.

On the other hand, flat tail bullets do not mind the longer jump to lands, and may be the ticket  when you can not long load to longer OAL to keep the bullet jump to lands under .008" on ignition,  and come out of the mag isntead.

So for boat tail bullets, figuring out the OAL needed for them to be at less than a .008" jump to lands (.004" is more ideal instead), and if you can use these loads out of a mag.
Step two is working up powder amounts to get the bullet to exit the muzzle at the end of either its barrel harmonic oblong whip points to make the barrel shoot it tightest.  Also that goes hand and hand with this, is watching the speed deviations of the loads, since the higher the deviations of speed of the load, the more the bullets are going to exit the muzzle before or after the muzzle harmonics end still sweet spot isntead.