I prefer to use a separate target for darks/flats/bias (actually just flats as I use libraries for the others.)
Then when you just want to take the calibration frames just disable the other targets in the sequence and that should stop those annoying messages from popping up. What is happening is SGP sees that you have light frames active and will attempt to validate the options for the sequence. If no light frames are active SGP will skip this validation and just take the calibration frames.
Thanks,
Jared