Chuck,
I have played a lot with and without my bipod and yes your POI can change because of the bipod- more so when shooting prone. Obviously check to see that your barrel is properly free floated, shooting prone with a bipod can put downward pressure on your gun causing a pressure point which could be the problem. Maybe you need more clearance in the barrel channel?
When I shoot from a bipod I try to put some forward pressure on the bipod legs (preload) with my shoulder. When I shoot long range this significantly tightens my groups.
With any McMillan stock I don't think that stock design would have much to do with your problems as they all have stiff forearms as you know.
Hope this helps.