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The first thing I would try would be to stack and process just the lights, ie don't use the darks at all. If the artifacts still show up, then you know that they are in the image. If not, then the darks are responsible.
Drift is not an issue. Darks just remove dark current at particular positions on your camera sensor. It doesn't matter what is being imaged or where it is on the sensor.
Geoff
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