Mark,
in order that alignment works correctly, CFA images of a DSLR camera or an OSC camera always have to be debayered (to yield a RGB image) before the alignment step. I don’t know DSS (I am using PixInsight, and Vince wrote that he does too). In PixInsight you can execute the steps separately and nobody prevents you from doing it in a wrong sequence. If DSS performs these steps in sequence automatically, it will perform them in the correct order, just as it did before.
Bernd
Hi,
Bernd is absolutely right for me. Debayer before Align makes a lot of difference to the image. I still end up with a red cast but it is even across each frame instead of a multi-coloured image.
Mark for the flats issue I am unsure it will make a lot of difference but I will try to do a new set of flats and see if it will solve the problem completely. I can’t comment on DSS as I use Pixinsight. I never had this problem when I was using the ASI071. It only started when I use the Pro version.
You are absolutely correct that discussion needs to move to ZWO forum as I honestly don’t think it has anything to do with SGP.
Thanks again.
Vince
Hi everyone, I just experienced the same issue with my ZWO 071 camera. From a 50 light frame sequence, I have 28 bad frames with a green cast in the background. The other 22 are fine. All 50 frames were obtained the same night, in the same sequence.
I am worried I could have lost this frames. It`s a lot of data, and this is only one target. I did 21 more in a two night session with a C8 and a hyperstar!
I`m attaching a bad frame, and a good one so that you can compare by yourself. Everything was bayered with Pixinsight, with RGGB bayer pattern. Bayered frames look exactly the same (FITS Format).
This is the first time I experience this problem. I think it has something to do with the bayer pattern.
Hopefully someone could help me out with the solution!
Thanks! 
I think I just solved my problem. Apparently SGP didn´t wrote the CFA values for some of my frames (that would explain the greenish cast on some of them).
The greenish cast appears whenever I calibrate my files with Pixinsight`s Image Calibration Module. This module has a checkbox by default, with 3 commands: “CFA Detection”, “Force CFA”, and “Ignore CFA”.
The greenish cast dissapeared with the “Ignore CFA” check on, after running a calibration with Darks, Flats and BIAS. Once calibrated, I run the Debayer process, and every frame was fixed. All my frames where correctly debayered! 
After that, everything else went smoothly!
Hope this helps anyone!
