Hi Francesco
I'm getting a similar issue both with BPP and with the Image Calibration tool. Perhaps understanding how the flats are applied would be good to know.
My issue began when I created some master flats in SII and Halpha and OIII using a QSI690. I've noticed that the SII and Halpha flats have "diagonal" striations on them which, so far, I understand from reading various forums, is some kind of artefact of the chip visible at certain wavelengths. However, assuming that the whole purpose of flats is to pick up this kind of thing and then eliminate it by applying to the subs after bias and dark subtraction, I was not too concerned at first. I assumed that the BPP and IC tools would be somehow doing ( median(flat) * calibrated sub / flat ). However the resulting images CLEARLY show the diagonal striations - almost as though they have been amplified rather then eliminated. This is apparent when I use BPP and IC but not when I use PixelMath to apply the flat division.
Interested in anyone knows anything about this or can explain - maybe I should direct my/our question directly to the developers (who, by the way, have created a superb product in PI!!!!)
Steve