An approach to investigate the effect of system uncertainty on the optimal controlconfiguration selection in multivariable systems is proposed. An optimal control configuration,i.e the configuration which best agrees with input-output pairing rules according to certaininteraction measure (IM) can be obtained automatically by formulating the control configurationselection as a Transportation Problem (TP). The proposed approach then checks whetherthis optimal control configuration is valid for given system uncertainties or if a change in theconguration could be expected.