Granular films SiO2(Co) exhibit unusual magnetic and magnetotransport properties which are strongly dependent on the composition of the film and material of a substrate. For example, the injection magnetoresistance (IMR) coefficient reaches a giant (GIMR) value of 105% at room temperature in SiO2(Co) films on an n-GaAs substrate. However, the IMR effect is negligible in the case of a similar granular film deposited on the n-Si substrate. In this report, the structural and magnetic properties of granular film SiO2(Co) on Si substrate are studied with the aim to understand the cause of the difference in IMR coefficients for SiO2(Co) thin film deposited on n-GaAs and on n-Si substrates. Investigations were carried out using complementary methods of Polarized Neutron Reflectometry, Grazing Incidence Small-Angle X-ray Scattering, X-ray Reflectometry, Scanning Electron Microscope, and SQUID magnetometry. It is shown that the interface layer between the granular film and Si substrate exhibits metallic rather than magnetic properties and eliminates the GIMR effect. This interface layer is associated with the Si diffusion to Co nanoparticles and the formation of the metallic cobalt silicides.