I'm not sure if this is relevant your situation but I experienced a similar effect with my groups shooting prone with an Atlas that I had mounted on my 300WM. My standard rifle hold with all my rifles is to apply forward pressure to the bipod, moderate(5-10#) rearward pull on the grip, and a very light cheek weld. Prior to mounting the Atlas I had been using a Harris bipod an all my LR rigs including the 300WM mentioned above. With the Harrus I had no issue replicating accuracy of .5MOA irrespective of shooting position with the exception of a very repeatable elevation adjustment of +.25MOA when moving from an upright(bench or sitting), to a prone position. This was consistent with all my LR rifles. When I changed the 300WM back to my Harris, my previous accuracy was restored. Because this seemed strange, I decided to try the Atlas on my 6.5x284 which I had been shooting for a few years with a 9-13" Harris. Same effect as seen on my 300WM. The only thing that I could surmise was that the "play"in the legs of the Atlas compared to the more rigid design of the Harris might have been introducing some form of barrel movement.....but I'm not sure. In any case, I decided that I wasn't going to modify my well established shooting style, and just decided stick with the Harris.