When calibrating the flats using the ImageCalibration process, you can either enable the 'Master Bias' section and select the MasterFlatDark with option 'Calibrate' disabled (in the appended screen sction: left) OR enable the 'Master Dark' section, select the MasterFlatDark with options 'Calibrate' and 'Optimize' disabled (in the appended screen sction: right). These settings are equivalent.
Bernd