The new SmartSmoker Pro allows you to switch the power going to the motor, to come from either the receiver battery, or a separate "isolated" and dedicated battery for the pump. Not both. In either case the SmartSmoker Pro needs a tiny amount of power from the receiver in order to run the microprocessor in the controller. So this receiver power must always be present. The external battery cannot be powering an ignition system or anything else while connected to the SmartSmoker Pro since a ground loop may form possibly bypassing the motor control.
The power source select jumper must always be connected to the center pin. When viewing the SmartSmoker Pro label the jumper must connect the center pin to the right most pin to make the controller use the external battery for pump power. To make it use receiver power it must connect the center pin to the left pin with the jumper.
The external battery connector as you have seen is removable. If you remove it you must insure that the bare exposed connector pins are taped up and insulated. Otherwise contact with any electrical potential can damage your pump.
If none of the above seems to be different than what you have been doing then the only other thing that could be wrong is that the connector to the external battery has a break in it somewhere. The external cable can be flipped 180 degrees and plugged back into the bare pins. It is wired so that there is no wrong orientation but you will be using a new pin by flipping it. If you have a spare servo extension cable try substituting it for the one included with your pump to see if the cable has a break. If none of the above solves the problem then please return it to us and we will test it to make sure nothing has changed.
We do not use spot testing in our factory. All of our units are 100% tested before they are shipped. In the past the only thing that gets by are intermittent connections that somehow go permanent when they get to our customer. Either way you have our full support and warranty.