yeah, that's right - i'm reasonably sure everything (lights, flats) in BatchPreprocessing gets calibrated with the darks or master dark.
this is probably not appropriate for the flats... so what i've been doing over the last couple of days is making my own master flats which have been integrated separately with a matching master bias. i shot my flats at iso100 (vs 1600 for the lights), so i have to do this.
i can't tell if the script is hardcoded to output monochrome CFA master calibration frames, or if i accidentally told it to do that. but my master dark and master bias (iso1600) were in mono CFA format, so i had to make my new master flat like that. so i configured DSLR_RAW for mono CFA (is there a format hint that does this? "raw" gives me an RGB bayered image), then made my master flat bias, calibrated the flat subs with it, and then integrated the flat subs into a master flat.
then back in BPP i select the 3 masters and tell it to use masters rather than to create them. i think this is "safe", meaning the script does not try to calibrate the master frames (i hope).
the BPP script is a godsend but it does need some more improvement, especially in this department. even if you are using a mono CCD it's likely your flat exposures are short and need a different dark. and if you are using a DSLR and use low iso for the flats, same situation...
now of course for some reason the debayering in the BPP script is choking on my calibrated lights (which are now mono CFA). they are fine though - they can be debayered with the Debayer process, and then registered manually and integrated. i'm not sure what's causing this. i tried unchecking "CFA" but then my dark scaling went wild (huge values.) that's usually an indication that something went wrong with the debayer process, so i think it needs to be checked.