“Windsor Sigma Clipping at 1.0 and 3 iterations. I was just trying some rather extreme settings as I want to get rid of as much background as possible to try and combine the comet and stars later.”
Winsow clipping 3 iterations kappa 1? Why a kappa of 1? This will reject 1/3 of all data, so good data as well?
Outlier rejection filters will not get rid of background, it will get rid of outliers. Depending on the specific dataset this can have all sorts of unwanted effects if you set the filters too aggresively.
Remove backgroung should be done with the remove light pollution tool I would suggest ;-)
(In the case of more than 30-40 frames, you probably should never set the kappa below 2 I think for outlier rejection. Above 3 is also pretty useless if you have plenty of frames)