The 3" barrel should give you a little better performance than the 2" in general. But I am going to guess that many of the tiny variables that exist from round to round and gun to gun (and possibly even plastic milk jug to plastic milk jug) lined up in favor of the Charter Arms and against the S&W. Most likely if you were able to repeat this test a lot more times you would see diffrerent results.
It would also be interesting to chronograph the round as you were testing it for penetration, i.e., have the chrono between the gun and the milk jugs to get an actual reading on each test.
"No matter where you go, there you are." Buckaroo Banzai