Over the past decade, developments towards near-infrared (NIR) optical tomography involve the recovery of interior optical maps from boundary measurements using the first principles of light propagation models. The refractive-index mismatch parameter in the boundary condition of the light propagation model, namely the diffusion equation, can significantly impact model prediction of measurements and therefore image recovery. In this contribution, the influence of refractive-index mismatch parameter between predictions and referenced measurements of fluorescence-enhanced frequency-domain photon migration (FDPM) are established; its greater influence on emission over excitation predictions are demonstrated, and the methods to accurately determine refractive index mismatch parameter from basic principles are reviewed.