First, you cannot over power a gun if it still has the Fuse assembly in the Gun, the reason for the fuse is to safeguard the motor and GB internals, if you have a short, or reverse poled battery, or a short in the battery itself. Your guns are able to withstand alot more Power than what the manufactures are leading you to believe.
Check the connetion on the larger battery, sounds as if you have a weak contact, or a loose cell bridge in the battery itself, or a bad cell.
If possible check it on a volt meter, then hook it up to the gun, and check what you are getting to the motor.