The variation in intensity of molecular peaks in inelastic tunnelling spectra of formate-doped Al-alumina-metal tunnel junctions has been studied for a range of top electrodes and for a series of junctions roughened by prior deposition of CaF2 films of varying thickness. Intensities were found to decrease for different top electrodes in the order Pb, Ag, Au, Sn, In, Cuand Al, the last giving no measurable spectra, and to decrease with increasing junction roughness in the case of Pb. These results are successfully and coherently interpreted in terms of a detailed model of the metal-formate-alumina interface. This model takes into account the structure of the alumina, the packing of formate ions, and the interfacial and surface energies which, together with size, determine the structure of the top metal electrode at the interface.