I have no idea about the answer to your questions, but I see a difficulty that may make it tough for others to tell you as well. In both cases, the lighter looking chip has a black background as opposed to the darker chip against a white background. It is what I would expect to see if the two scans were of the same exact chip. I would scan the chips with the same background color. The different backgrounds can make the chips look lighter or darker. I am not sure at all by looking solely at the colors of these chips that they are different. The best bet is to scan the chips you are comparing together, to make sure the lighting is exactly the same.
Just a suggestion.
Michael Siskin