We report on electronic transport calculations for self-assembled mono-layers (SAM) of 1,4phenylene diisocyanide on Au(111) contacts. Experimentally one observes more structure (i.e peaks) within the measured conductance curve for this molecule with two cyanide end-groups, compared to measurements with molecules having thiol end-groups. The calculations are performed on the semi-empiric extended Hückel level using elastic scattering quantum chemistry (ESQC) and we investigate three possible explanations for the experimental findings. Comparing the experimental and theoretical data, we are able to rule out all but one of the scenarios. The observed additional peaks are found to be only reproduced by a mono-layer with additional molecules perturbing the periodicity. It is conjectured that the weaker coupling to Au of cyanide end-groups compared to thiol end-groups might be responsible for such perturbations.