Hi Chris,
it´s hard to say. What´s going wrong with the flats, when you use the BPP?
I had problems with the BPP too. My fault was, that I used not the same ISO as for the lights. The script uses the "light"-darks for the flats too, if you do not load extra flat-darks in the darks section and I think the ISO is not scaled right. The same problem is with bias. So it is better to use the same ISO. If you load extra flat-darks, the BPP uses them automatically for the right pictures. With DSLRs it is better to make flat-darks, even it is not necessary, because you can not deactivate the dark-calibration in the script. So the script uses the wrong darks and wants to scale them. With CCDs this works well, but not always with DSLRs, because the DSLRs are not as linear as the CCDs.
I hope that helps, but maybe your problem is different.
Greetings
Tobias