Outback,
How much lateral movement does the front take down lug of the upper have between the lower front ears. Is the front of your lower/upper rock solid, or is there sideways slop.
On most of the accuwedges that I have installed, you dam near had to stand on the carry handle/upper to get the two to mate (allow the take down pin to glide threw). Unless your wedge was an aftermarket knock off, you shouldn’t be able to add a shim (even on a low shelf receiver).
The only thing that comes to mind is if the front of the your upper is loose at the front of the lower (front take down pin), then you may have gotten upper shift at trigger pull, And, when you tightened the two up more with the extra shim, this is keeping the upper from moving around at the front of the lower (not very likely, but this movement will effect a questionable scope).
On a scoped rifle, the more you can dampen the buffer impact/rifle jarring, the less likely the scope zero will be affected (focal bracket bounce). An item that you didn't touch on is what brand of scope you are using. On some cheaper scopes, the simple jarring of the rifle can cause the scope to change it zero point, and would explain the flyers.
To give you an example, I have an ongoing bi-yearly battle on a Simmons scope that I bought years ago (6x18). About every six months, I have to send the scope back for replacement, due to not holding a zero. Originally, I picked the scope up for a 22lr, but the scope found it's way onto one of my flat tops, and the ongoing replacement s of the scope has become one of my running jokes/boil on my ass, kind of things. The only reason that I still have it is that they keep replacing it for free, or I would have thrown it away years ago.
So if your scope is in question, then maybe the extra shim just slightly deadened the carrier blow/upper jumping around on the lower, and this limited dampening is just enough to prevent the scope from loosing it zero point.