We investigate the accuracy of two expressions for configurational temperature when calculating thermal transport properties in non-equilibrium systems under thermal gradients. The temperature TconF, introduced by Jepps et. al [Phys. Rev. E 62 4757 (2000)] is found to give results in almost exact agreement with the equipartition temperature for the thermal conductivity of the Lennard-Jones fluid, and for the temperature profile across a solid-liquid interface. Measurements of TconF are, however, less precise than those of the equipartition temperature, which results in less accurate measurements of the interfacial thermal conductance across a liquid-vapour interface. The approximate expression Tcon1, which depends strongly on the number of sampled atoms, predicts unphysical negative thermal conductances in liquid-vapor interfaces, highlighting the limitations of some definitions of the configurational temperature in the computation of thermal transport properties via non-equilibrium simulations.