We present experimental evidence of modification of O2/N2, Ar/N2, 29N2/28N2, 34O2/32O2 ratios and CO2 mole fraction in dry air standards resulting from gas handling. Correlated variations among high precision measurements of multiple molecular pair ratios show diffusive fractionation to be the main modifying process. This mechanism can account for much of the previously unexplained CO2 instability commonly observed in air standards used by the atmospheric CO2 measurement community. Identification of the effects of diffusive fractionation helps to isolate effects of other processes such as surface adsorption, which is also implicated as a cause of CO2 modification in some applications. These findings have direct implications for the preparation and maintenance of O2/N2/Ar and CO2 calibration standards and are relevant to other atmospheric measurement activities that involve gas handling.