This may have been covered....if I missed it, I am sorry.
Now, you say that your scope is mounted correctly as far as scope cant and alignment.
Now, with your gun FLAT on the rest and with a plumbed line on a target at 100 yards, shoot a group......dial up 25 moa, shoot another group......does you scope go strait up, putting the group ON THE LINE.
In other words, is the INTERNAL adjustments you are making with your scope equal EXACTLY what you are looking for on target. Is the dialed up group off to one side of the line......1 inch @ 100 = 10 inches at 1000. I have seen a scope that, when dialed up, went to the left. Someone, somewhere, told me that this was not possable. IT WAS!! And that scope was on strait and mounted correctly. But, it was a "bargan" brand scope!!
Just thinking more about this....you shouldn't even need to fire any groups. Just make sure the gun DOES NOT MOVE when you are making the adjustments. You should be able to watch the scope track up the line as you dial up. I know that it is easier with a flat bottom BR stock than a hunting stock.
I guess to be sure I would shoot actual groups. That would be my BR tendancies rearing their ugly head again.