It looks to me as if the temperature of the darks does not match the lights. I do not use Pixinsight to calibrate, but I would see this from time to time with my DSI-III & Nebulosity. Scaling darks did not work well due to the amp glow of the camera. Even when I used it with the amp turned off, scaling darks was iffy...I'm not sure why...probably because the DSI-III is not temperature regulated and a set of darks could have temperature variation in themselves as well as the lights.
Steve