Oxygen vacancy centers in buried oxide (BOX) layers of Si/SiO2/Si structures produced by implantation of oxygen ions into silicon and subsequent internal thermal oxidation (ITOX) were studied by monitoring hole trapping and paramagnetic properties. During the ITOX process the BOX layer is augmented by thermally grown oxide. We have found that this additional buried thermal oxide layer has nearly the same density of O vacancies as the initial buried oxide, and an even higher number of oxygen vacancy clusters (E-delta' centers), even though the superficial Si layer was saturated by oxygen. This result suggests the generation of oxygen vacancies in Si-confined SiO2 to be due to temperature driven interaction between Si and SiO2. The clustering of the oxygen vacancies observed in all the high temperature oxides (both buried and unconfined), and the inverted relationship between the vacancy charge and its paramagnetic state point toward changes in the SiO2 network structure as compared to the conventional oxides.