As a check try the same measurement with just a pad. Try a 3 or 6 db whatever pad you may have on hand. The suspect area I believe is either source or load termination either from the vna or the sa. One of these devices is NOT providing a proper 50 ohm termination. Under the assumption that the filter is designed to be source and load terminated into 50 ohms, if these terminations are not proper, than the loss will be off between the measurement devices. The experiment with the pad may provide a clue as to what is producing this error.
