I am not sure what the issue is with your scanner but I can tell you that many scanners have problems with certain colors typically Red and shades of Red through Orange. If I remember right without getting too technical about it... objects are the color that you see because of the frequencies of light that are reflected and absorbed by that object. Scanners use artificial light and the frequencies are not the same as what you see with your eyes. The solution would be to either get an expensive scanner or use a camera on those type chips. I hope that helps?
Typical ORANGE color chip with scanner: