It’s hard to tell… there are so many different options that can change the behavior of SGPro. If you want to either attach your sequence to this thread or submit logs showing the run, we can guide you in the right direction. Without looking, I’d say that you should inspect target settings for the target containing the flats. SGPro does not know a target only contains calibration frames or not and will always honor target settings dictating whether or not it should attempt to center on a location when it starts.
Guidance for submitting logs is here: How to Submit Logs in SGPro