Hi Guys I appears that you all think that it maybe the Flats, and/or the way they are taken, so we will go there first.
I take Flats, usually on each evening of imaging, fresh ones so to speak.
I wait till after sunset, about 15 minutes, take 16 images at the same ISO as my lights will be, using the AV setting on the 5D, with the scope pointed straight up into the dull blue heavens.
Once captured I Medium Combine then in Image Plus, when the process is finished, I end up with a master flat, use Luminance and Gamma setting to grey scale, and there you have it.
This Master Flat is then mixed in the auto imaging process in Image Plus, with the lights, and so the process continues.
A combined image is created, as you all are aware.
Paul, to your 1st question, the answer is no, nothing changes in the imaging train.
One Master Flat attached, done two days ago.
Leon