I recalibrate my Canon scanner for almost every new scan, but especially if I'm changing from transparent to opaque watercolor or if the new piece has a different white level than the last. It's under image settings on the advanced mode of the ScanGear software. You can also adjust brightness, contrast, color, etc. there. I also have to allow for the difference in monitors. I work with three different monitors and they all display images differently.
Some colors have always been problematic. Even back in the old days of color separations for printing, certain reds used in illustrations would always behave strangely in scans.
"All black and white, nice." ~ golders