they are probably calibration artifacts; I assume this is a narrowband image and as such the background is probably not much different than a dark. what happens is the master dark is a more precise measurement of the dark current in the sensor, and when you subtract that master dark from a subframe, there are pixels in the subframe where the dark current was lower than the average and as such the calibrated pixel would have a negative value... which gets clamped to 0 by imagecalibration.
so you then have these patterns of 0s in your calibrated frames, and when they are registered, tend to give you a moire pattern like you see in your image.
to see if this is your problem, you can open one of the calibrated subframes and apply the pixelmath expression iif($T==0,1,0) and you'll get an image where every pixel in the original image which is 0 is marked with a bright pixel. in a well-calibrated image you should get an all-black image after applying that expression... if you see a bunch of pixels lit up then you probably have the problem I am describing.
to get around this, you can add an output pedestal when calibrating the lights, try 100 DN or 200 DN or so and see what happens.
rob
