I don't have a very good answer, but I see the same thing in the scanner reference files as well as the camera references. And negative RGB values show up in the references for the regular ColorChecker too. All I can guess is that originally the references were made using something that applied RGB values to a certain gamut, and so the negative numbers and the >255 numbers represent what is outside of that gamut? Or something?
Check this out on Bruce Lindbloom's site: http://www.brucelindbloom.com/index.html?ColorCheckerRGB.html