If the butane is burning in the smokebox, that indicates to me that there isn't enough air mixed with the butane for it to burn in the poker burner.
I apologize if the following suggested steps are obvious to everyone and that these steps have already been tried.
First, does the burner work when removed from the locomotive? That is, does it generate a flame from all of the slots in the poker? Is the size of the flame controllable by adjusting the fuel valve? If not, there likely is a mismatch among jet size, venturi air vent size and poker length/number of slots.
Second, try opening up the choke in the side of the venturi tube to allow more air to enter the burner and mix with the butane. Also, reduce the butane valve opening to be sure that the butane supply isn't overwhelming the air supply.
Third, be sure that the jet outlet is located around the center of the venturi air inlet hole to that air is being sucked into the poker burner and not pushed out.
Fourth, try a smaller jet size so that the butane stream has time to mix with the air to allow combusion.
Fifth, see if there is a clear hole or path to allow air to enter the flue from the poker-end of the flue. On Accucraft models, in addition to the air holes and choke that allow air to enter the inside of the poker burner to mix with the butane, there sometimes is a hole, drilled through the jet holder flange that allows additional air to enter the rear (jet end) of the flue, between the outside of the poker burner and the inside of the flue.