If you are using a vertical tank, don't install an anti-siphon. The vertical position is ideal for keeping CO2 out of the ASA. Anti-siphon tubes are generally used on horizontal or bottles that are tipped back on an angle.
The gas contained in the dump chamber will have more mass when using CO2 than when using compressed air. This won't manifest itself in much of a difference in the actual velocity, but the farther you get from ideal operating conditions, the more effect it has. A few fps difference in velocity can be quite a bit more force on the ball in the chamber. That could be the difference you are experiencing and it might just be enough to get past the breaking point of the balls due to the faster acceleration of the bolt. The mass density of CO2 is 1.5 times higher than compressed air at operating temperature. Since the energy transfer is directly related to the mass of the colliding objects, CO2 has a greater ability than air to transfer its energy to the ball at any given pressure. It won't be 1.5 times greater, because its mass also works against it causing the gas to be less responsive due to acceleration of the heavier gas through the air passages (the bolt). In the end, it does provide some increase in energy transfer. As mentioned above, the longer barrel will help because of the slower acceleration rate of the CO2 gas. This will allow you to turn down your velocity (pressure) setting and achieve the same velocity results as with the shorter barrel.
Except for the Automag in front, its usually the man behind the equipment that counts.