PROC REG constructs only one crossproducts matrix for the variables in all regressions. If any variable needed for any regression is missing, the observation is excluded from all estimates. If you include variables with missing values in the VAR statement, the corresponding observations are excluded from all analyses, even if you never include the variables in a model. PROC REG assumes that you might want to include these variables after the first RUN statement and deletes observations with missing values.