The reason is this for the small current.
# sc 11 : q = -0.00005 e Etot = 29480.98483 Ry dRho = 6.1049E-08 dEtot = 7.1669E-06 Ry
The charge has left the central region and disappeared into the electrode reservoirs, and hence you have
created a 1-dimension quantum barrier, and it is very effective at terminating the transmission.
In general when a system looses all it charge into the electrode reservoirs, there is a serious problem with the parameters,
and hence it requires more convervative parameters, but in your case I would personally start by making these two
# -----------------------------------------------------------------------------
# TwoProbe Algorithm Parameters
# -----------------------------------------------------------------------------
Electrode Constraint = ElectrodeConstraints.Off
Initial Density Type = InitialDensityType.NeutralAtom
into
# -----------------------------------------------------------------------------
# TwoProbe Algorithm Parameters
# -----------------------------------------------------------------------------
Electrode Constraint = ElectrodeConstraints.DensityMatrix
Initial Density Type = InitialDensityType.EquivalentBulk
And then I think you will have solved your problem.