I'm running into the same problem with my Geeetech A10M + Cura.
I have attached a sample file exhibiting the problem. I have yellow color mounted on the second extruder, so I sliced this yellow model to be printed using the second extruder. However, the nozzle turns off after printing the skirt.
I will look into the source code next to find out where the erroneous M104 is emitted.
In the meantime, a workaround is to run a postprocessing script that replaces "m104 t0 s0", "m104 t1 s0", and so on, with an empty string.
CFFFP_fuesse_schnabel.gcode