Yes, this is a common experience that the callibration frames are not quite right and create problems rather than solve them.
If you have a light-polluted sky at all then flats are much more important than darks; also if there is any vignetting (uneven illmination) in the system at all.
I’ve never had success with artificial flats (using a light box for example) but find the best method is to take flats on a clear sky at sunset or slightly earlier. The optical system needs to be focused and ideally pointing in the same direction as for the light frames (in case there is any mechanical slop).
With a DSLR it’s fairly important that the dark frames are taken at the same temperature as the light frames (to within, say 3 degrees C). I always note the temperature, and have built up a library of darks taken at different exposures and different temperatures.
Anyway that’s a nice shot. I’ve got an ED 80 and it’s a good combination with a DSLR.
David