Diverse spectroscopic methods operating at radio frequency depend on a reliable calibration to compensate for the frequency dependent damping of the transmission lines. Calibration may be impeded by the existence of a sensitive interdependence of two or more experimental parameters. Here, we show by combined scanning tunnelling microscopy measurements and numerical simulations how a frequency-dependent conductance response is affected by different DC conductance behaviour of the sample. Distinct and well-defined DC-conductance behaviour is provided by our experimental model systems, which include C60 molecules on Au(111), exhibiting electronic configurations distinct from the well-known dim and bright C60’s reported so far. We investigate specific combinations of sample electronic configuration, DC bias voltage, and radio frequency modulation amplitude. Variations of the modulation amplitude as small as only a few percent may result in systematic conductance deviations as large as one order of magnitude. We provide practical guidelines for calibrating respective measurements, which are relevant to RF spectroscopic measurements.