The force acting on the ball is also acting on the front of the bolt. The bolt is held forward by whatever mechanism that pushes it forward. It could be a mechanical mechanism or pressure. It doesn't matter much. It is essentially part of the gun. However, the ball mass is much less than the mass of the gun so the ball moves away from the gun. The equal force is still pushing back though. The force that is propelling the ball is also propelling the gun. No matter how you slice it, that energy has to go somewhere. If you were to place your hand at the end of the barrel and it got hit by the ball, it is the same amount of energy that the gun is moving back into your firing hand with. Its just that the gun with its greater mass does not reach the same speed. Therefore, the perception is that firing of the ball does not produce much kick. This is also partially offset by the fact that most guns start to release air as the bolt mechanism is moving forward so the stopping of the forward motion as the bolt changes direction (energy transfer forward) offsets the push backwards by the air firing the ball.
The moving mechanism in the gun can sometimes be a major part of the mass of the gun. When this mass moves back and forth, it does affect the movement of the gun. The backwards motion is the kick that most people feel when they fire a paintball gun. The forward motion as mentioned above is somewhat offset by the firing of the ball which is why the guns don't kick forward before they kick back. The backwards motion of the bolt and mechanism causes pushes the gun to kick back when the mechanism comes to the sudden stop at the end of its travel. The reason most paintball guns kick the barrel up in the air is due to the gun rotating back across the trigger hand which acts like a pivot point.
As mentioned by others, as the mechanism and bolts get lighter and as the mass of the guns get lighter, the mechanical effect is reduced and the recoil due to equal and opposite force given to the ball-gun combination becomes a greater part of the equation..
Except for the Automag in front, its usually the man behind the equipment that counts.