Yes. Uncontrolled recoil has effect. It is a physics problem most undergraduates do (throw something heavy on ice, two bodies move in opposite directions, energy spent sliding the thrower is removed from the projectile due to conservation of energy, etc). The question is not whether it does, but to what degree?

It looks like youre measuring muzzle velocity with a device mounted to the barrel. If that's true, i suspect it almost entirely negates the difference you are looking for because the rifle recoiling adds perceived muzzle velocity that the target (and the rest of us) do not experience.