Is the rifle loose perhaps? I had an experience with a drilling that shot lower and lower the looser it got. And I hear that Chapuis double rifles do tend to shoot loose after a while.

The other factor is that as the bores shoot in, barrel residence time is shorter so the gun will tend to shoot lower and crossed. (The bullets exit earlier in the recoil motion).

Adding a pad could exacerbate this by allowing more straight back recoil and less deviation to the side.

You can try a heavier bullet (someone makes a 300, can't remember who) or a faster powder to try to offset the crossing. You need to go in the direction of MORE recoil, not less, to offset crossing.

Frankly, if the rifle shoots around 2" at 100 yards, it's better than 80% of the double rifles out there so either let it be, or sell it and buy yourself a modern bolt rifle. Your first group could be a fluke, 2 shots from each barrel is NOT statistically significant, not by a long shot. Heck, it wasn't long ago when 3" from a big game bolt rifle was considered accurate.