Hi Pelle,
I remember you from Cloudy Nights forum. Have you tried other capture software like Nebulosity? I don't have your issues with Nebulosity. You can try Nebulosity for free. You can test it indoors. The free trial of Nebulosity will purposely draw diagonal lines across the image. If you pay for it and input the license number, the diagonal lines will disappear. But your purpose is to test for the black column and diagonal lines will not be in the way.
If you still get black column with Nebulosity, then you should contact Atik.
Peter