We present an analysis of wave propagation in a two step-index, parallel waveguide system. The goal is to quantify the effect of scattering at randomly perturbed interfaces between the guiding layers of high index of refraction and the host medium. The analysis is based on the expansion of the solution of the wave equation in a complete set of guided, radiation and evanescent modes with amplitudes that are random fields, due to scattering. We obtain a detailed characterization of these amplitudes and thus quantify the transfer of power between the two waveguides in terms of their separation distance. The results show that, no matter how small the fluctuations of the interfacesare, they have significant effect at sufficiently large distance of propagation, which manifests in two ways: The first effect is well known and consists of power leakage from the guided modes to the radiation ones. The second effect consists of blurring of the periodic transfer of power between the waveguides and the eventual equipartition of power. Its quantification is the main practical result ofthe paper.