Thanks, I have added one FITS and one CR2 light frame to the same folder.

I'm somewhat surprised by your comment about my flats. It was my understanding that it was best to let the camera choose the exposure when pointing at the flat panel (light source). When I do that, my camera selects 1/4000sec. I then selected that in Ekos.
The next higher exposure setting seems to be 1/100 (0.001sec). When I use that the flats are over exposed. When I open the CR2 flat it looks good to me (if a bit blue-ish), but I'm by no means an expert... ;)
Is my flat panel too bright? It's an old LED TV with the display removed and only the backlight left, which I made remote controllable. It is mounted on the wall in front of the telescope when it's parked.