Ah yes. I completely forgot about the whole 3D vs 5D gcode thing. I haven't had to deal with the old style gcode since I upgraded my Cupcake CNC to a stepper extruder. Is such a thing possible with a BfB?
You could always try using another slice engine within MatterControl. However, as far as I can tell Cura and Slic3r won't do 3D gcode anymore either. If all else fails, you could generate a gcode file using some other software (Skeinforge?) and still print it through MatterControl.