I have this same problem as well, and I was wondering if anyone actually knew why this happens. Let me outline quickly my problem as it might differ slightly from the original poster's.
I have about 30 registered frames, all but one of which have some sort of black border due to registration. About 1/3 of them, when used as a reference frame bring the median up by about a factor of 4.5x (not all 4.5, some 4.2, some 4.3, etc.). Some, however, leave the median the same. To debug, I was using only Additive normalization, no scaling, no rejection of any sort, so aside from averaging the frames, there should not be any further calculations except the normalization.
The additive normalization formula looks to take the pixel value from the current frame, subtract the current frame's median, then add the reference frame's median. I did the calculations manually for a number of pixels, and there was no way that I could reproduce even close to a 4.5x increase in value of each pixel.
I suspect that this has something to do with the registration's 0 value pixels around some of the edges, but I cannot see how and why. I cropped the same images and they stacked exactly as would be formulaically expected. Even when I clipped the 0 value pixels out, the median of each image did not change very much; certainly not enough to increase pixel value by 4.5x.
I am aware that, at this point, I can just use a different reference frame to make everything more to my liking, but I am now curious as to what is going on under the hood. If anyone is curious, I have included a link to a number of the frames in my Dropbox.
https://www.dropbox.com/sh/6eeh8dwzt3x5904/AAA16HxeF0aBSl7Y8ISONPpXa?dl=0Thanks in advance,
-John