The scattering region takes the k-point specification from the electrodes in the X and Y directions (or, rather, A and B, as defined by the electrode unit cell vectors). In the Z (transport) direction, however, there is no periodicity. This is the whole point of the open boundary conditions that allows ATK to apply a finite bias across the structure; electrons flow through the system which is in non-equillibrium.
During the initial "equivalent bulk run" which is turned on by default, the system (Left electrode + Scattering region + Right electrode) are turned into a bulk system and run as such for the purpose of creating a better initial guess for the density matrix that that provided by neutral atoms. During this calculation (which can be turned off, and should be turned off if the equivalent bulk system does not fulfill periodic boundary conditions geometrically or parameter-wise, for instance in case of anti-parallel spin polarized electrodes), the k-points are (NA,NB,NC=1) where NA and NB are taken from the electrode k-point specification. There shouldn't be any need for k-points in C (Z, that is) since the system is quite long in this direction, and anyway the equivalent bulk calculation is just an approximate first step towards the real results.
