Think of where the energy that makes the ball shoot is coming from. Sure, the motor is supplying it - indirectly. But your spinning wheels act as mechanical "capacitors" - they essentially "store" the motor's power as rotational energy so that it can be transmitted to the balls. When you push the ball through the shooter wheels, you are taking energy from the wheel and applying it to the ball (remember conservation of energy, and in addition there are frictional losses as well). So the flywheel slows down until the motor can once again spin it back up to top speed. If you insert a game piece before the motor can bring the shooter back up to speed, there is less energy that can be transferred to the ball, so you get a shorter shot.
You have a few options on how to deal with this. You could simply wait long enough between shots so that the wheel can get back up to speed. Or, you could add more power to your shooter (a second motor?) so that the flywheel can be accelerated more quickly. Or, you can look at the equation for rotational energy (
http://en.wikipedia.org/wiki/Rotational_energy) and see if there are changes you can make to your shooter configuration that would result in less of a decrease in speed between shots (hint: "heavier" wheels take a longer time to accelerate, but they also decelerate less when you push a ball through. In this case, "heavy" actually means "high moment of inertia").