The Si2p binding and the Si-KLL kinetic energy difference between the SiO2 layer and Si substrate is shown to be influenced by application of external voltage bias to the sample holder due to the differential charging as was already reported earlier (Ulgut, B.; Suzer, S. J. Phys. Chem. B 2003, 107, 2939). The cause of this bias induced (physical)-shift is now proven to be mostly due to partial neutralization by the stray electrons within the vacuum system by (i) introducing additional stray electrons via a filament and following their influence on the measured binding energy as a function of the applied voltage, (ii) measuring the Auger parameter. It is also shown that citrate-capped gold nanoclusters deposited on the SiO2/Si system experience differential charging similar to that of the oxide layer rather than the silicon substrate.