The elevation difference tool will display, or generate images, based upon the settings that you select. For display those settings are located in the LAS properties -> Symbology -> Delta Z tab. The colors used by default usually indicate a good fit with green and a mismatch in red. Hence, open terrain areas generally appear green, while vegetated areas when comparing all classes typically look red since one cannot expect a point from two different flight lines to strike the vegetation at the same elevation. The general range of values for those colors can be seen on this display. The areas where you see the data colored by intensity are areas of the data set where no overlap between flight lines exist. The intensity color is used to complete the picture, but not obscure the focus from the observing trying to determine the match between flight lines.
Since the display tool is based upon the pyramids when not viewing the data at 100% it is usually better to use the Export Wizard to generate dZ images for review.