I suggest that you start working on this issue by running through a simple, manual calibration process. You'll want to first diagnose if your automatic process is inadvertently introducing or not removing the artifacts.
Make a master dark of same duration and temperature as your light frames.
When you take flats, where do you typically place the histogram in the range? This ought not to be too critical, but I have been advised with this camera to place it in the middle, even as high as at 2/3rds the full range. I tend to target the 1/2 position. I also like to take flat darks of same duration and temperature as the flat frames, but this also should not be too critical if you prefer to use bias frames.
I suggest you use these master frames for calibration, then register, then combine.
We'll see if that helps or if more diagnostics are to be done following this!