The sky is green, the grass is blue, and this is normal and expected.
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There any many active duty with thousands of rounds on these rifles that will tell you the same issue exists.
I ran into something similar to this, but it was operator error. Confirmed operator error. In my instance.
******TACTICAL PAUSE******
I'm not saying that it's not flex. If you look at it from a physics perspective, the only thing that holds the gun together is 2 screws clamping the barrel. The MRAD weighs 9kgs loaded. Is it possible for a 9kg weight to flex an aluminum chassis? I think so. And considering the barrel, and only the barrel, affixes to the chassis, instead of the receiver on normal guns, it makes sense to me that flex could change enough how either the clamping is working and/or how that clamping force is being applied to the barrel, changing POI.
Thats just a thought experiment. i'm not saying its the case.
Last year I changed it from a pure prone gun to a field gun. To do that i had to make changes to the stock's setup. When I say field gun, I need to be able to shoot this from multiple positions, including unsupported with a sling. The MRAD hates this idea and it's not made for it. We refer to the MRAD as a fair weather gun now. If it's nice and flat and prone. MRAD is fine. By trying to set the gun up once for all positions, I ruined it. Especially prone. I thought i'd actually broken the gun or there was some mechanical issues. It wasn't. It was me.
The problem ended up being the buttpad. If i didn't have that right smack bang where it wanted to be, my gun would throw rounds. Literally. I shit out a 4 MOA group at one point. As soon as I abandoned the "one size fits all" approach and went back to a dedicated prone setup, the gun went back to trying to 1 hole and I went back to ruining that for it.
As someone who's literally sat down with a medical protractor to measure arm angle and everything, I know that just by moving the LOP out 1 notch, it'll change my arm's orientation and just that little click will change my elevation between 1-2 mils. And I think what's causing the problems. Where flat or slightly shaped buttpads are more forgiving, when hte MRAD recoils, the shape of the buttpad causes it to slip in the shoulder until it hits a very specific point.
If you're not smack bang behind the gun in the sweet spot when the gun fires, when it settles in the spot it wants to be in, it usually causes a vertical shift. You can see that in my group, even the good one, I have vertical stringing. So if you don't have the rifle orientated exactly so that the shoulder is indexed into the buttstock exactly the same every. single. time. You'll get what you're seeing. Because this is what happened to me (albeit you at least can shoot a decent group).
I don't think it's flex necessarily, even though it makes sense to me that it could be an issue, I think what you've done by moving the forward support, is altered the recoil path into the shoulder. Your fundamentals are good which has held the groups together, but the way you have the gun setup isn't funnelling the recoil directly back into the shoulder like the MRAD needs. I think this is what is more likely to be causing the POA shift when the position changes. I could be wrong though.
This is my experience. It might not be the cause but just FYI that is what i've seen. The fact that there's so many posts complaining about MRAD POI shift, LOP etc etc to me suggests that, for the most part, this isn't the optimal solution.
Compared to every single other gun in the safe, the MRAD is EASILY the hardest to setup, hardest to use, and worst for varied positional shooting. Its the longest, heaviest and tallest as well. The short dudes completely loath it. I personally don't think it's a good design because of how hard it is to use and it kind of defies a lot of what we have settled on as a community for the optimal way to shoot a sniper rifle.
Maybe I'm old. Maybe i'm just shooting a dated way and we've discovered some new fangled way to shoot, and my enfeebled brain is too small to comprehend it (FIRMLY in the realms of possibility). I do realise that maybe i'm pushing this gun in a direction or use case that it's just not made for, but in my opinion, this is a step backwards. Other magnums like the Mk13 or even other guns in the ASR/PSR program like AXSR do everything better than MRAD. So I don't know how we got here, but if the world ended tomorrow, the MRAD would be the last gun i reach for.