Your charger is probably giving you a full charge, but your gun is probably overdischarging them during use. If you discharge below 3V you will damage them.
Are you running a Lipo monitor?
I set mine to go off at 3.3V and stop at that point. Because of the extreme current drains your gun can pull with each shot, at 3.1V, a shot can cause the voltage to dip well below 3V.