Check that your field strip screw isn't too long and bottoming out in the valve.
I have a pretty good idea that the proper pin setup is in place, but I have to ask the question anyway. Which emag pin setup are you using? Are you using the 0.712" pin and quad oring, or the 0.725" pin and regular urethane oring. The 0.712" pin and quad oring is the proper one to use.
Is the hopper pushing the paintballs too far into the breach area? This could be caused by using really small diameter paintballs.
What is the quality of your sear? If the RT action is too quick due to a worn sear, then the valve won't have time to properly charge the front chamber before it is trying to shoot again, which causes a short stroke result. The little puff of air caused by the short stroke is quite often enough air to push the ball forward but not fire it out of the barrel.
Except for the Automag in front, its usually the man behind the equipment that counts.