Colormap and mesh statistics

I am working on a project trying to find the differences between the right and left side of skulls. I want to see the differences in colormap, so I am using model to model distance. My problem is that on specific areas (like the area of the mandibular molars) I can see a difference between the 2 models when I superimpose the 2 models, but the colormap does not show me the same difference. For example, I can see after the superimposition that the molar in one model is more forward than the molar in the other model but the value on this area in y plane, after running model to model distance, is close to zero (which means no difference in the anteroposterior plane). Do you know why is this happening?

Thanks for your time!