If you take a look at the book "Quantum transport: atom to transistor" entitled by S. Datta, you will see that the electron flux from source to drain depends on the relative positions of the chemical potentials (i.e., the Fermi level) of source and drain as well as the energy level of channel. For example, please see the some pages of this book here:
http://books.google.com.sg/books?id=Yj50EJoS224C&lpg=PP1&dq=Quantum%20transport%3A%20atom%20to%20transistor%20googlebook&pg=PA8#v=onepage&q=&f=falseThe methodology implemented in ATK to handle the electron transport does not take care of the conductivity of electrodes.
Thanks to shifts in levels due to changing bias, can't we calculate any current throught the molecular device at some voltage values.
More properly speaking, the obtained current (I) may be zero, in other words, no electron flux from source to drain. Of course, the methodology in code is still valid.