Hey Jo, I found that the flats I was using were the cause of this rainbow gradient appearing when the data was stretched. My flats were of the dusk sky, so were blue, not sure if the colour of the flats had anything to do with it. Anyway, I simply restacked the image in DSS again but this time without the flats and the rainbow appearance was gone.
I follow the gradient removal process that Doug German goes through here;
http://www.youtube.com/watch?v=yTEVMH_WE80 its very simple and works fantastic. Hope that helps you.