Photoemission and low-energy electron diffraction studies of Au/n-type ZnSe(100) and Co/n-type ZnSe(100) interface formation show that room-temperature growth does not produce long-range order, despite the excellence lattice match of bcc Co, fcc Au, and ZnSe. Nonetheless, Au forms an abrupt interface without substrate disruption and grows in an approximately layer-by-layer fashion. In contrast, Co disrupts the substrate and the released semiconductor atoms dissolve in the Co matrix or surface segregate. Both metals induce slow changes in the Fermi-level position and give markedly different final positions, 1.29\ifmmode\pm\else\textpm\fi{}0.10 eV and 1.72\ifmmode\pm\else\textpm\fi{}0.10 eV above the valence-band maximum after 14 A\r{} deposition for Au and Co, respectively. Interlayer studies show that, when Co adatoms are deposited onto 4 or 8 A\r{} of Au on ZnSe, there is Co indiffusion to disrupt the buried interface, even though bulk Co and Au are immiscible. This Au-Co intermixing and ZnSe disruption induce changes in the direction of Fermi-level movement so that its final position lies between those of Au/ZnSe and Co/ZnSe. The deposition of Au over 4 or 8 A\r{} of Co on ZnSe alters the distribution of Zn atoms in the overlayer and again the Fermi-level evolution is altered. These results indicate that the Schottky-barrier height can be controlled through a proper choice of metals and interlayer thicknesses and that it depends on the metal adatoms, not the distribution of Zn or Se in the overlayer.