This is a bug, sorry about that.
The solution is to include these two lines in the script, after the definition of the gated two-probe method (i.e. insert this after line 243 in your script):
import NL
gated_two_probe_method._TwoProbeMethod__algorithm_parameters['initial_density_type'] = NL.DensityFunctionalTheory.ATKParameters.TwoProbeAlgorithmParameters.NeutralAtom
Hope that solves all your issues!