Yes, the problem are the settings for the light frame calibration. If you enable the section 'MasterBias' and select the MB, it will be subtracted from the light frames (step 1). Then, if you select the section 'Master Dark' with 'Calibrate' disabled, the MB will not be subtracted from the MD, so the uncalibrated MD will be subtracted from the light frame (step 2). That means both MB and MD are subtracted from the light frames, and this is not correct.
Correct settings:
Section 'Master Bias' disabled.
Section 'Master Dark' enabled, MD selected, both options 'Calibrate' and 'Optimize' disabled.
Section 'Master Flat' enabled, MF selected, option 'Calibrate' disabled
With these settings, only the MasterDark is subtracted from the light frames, then the result is divided by the MasterFlat and multiplied by mean(MF).
Bernd