Sorry, I didn't look carefully at the screen shots in your first post. Now I understand what you mean.
The prediction in your example is correct. It just happens that RGB histograms are always shown normalized. Normalization means that the R, G and B peaks are drawn with heights proportional to their relative amplitudes. The highest peak occupies the whole graph (vertically), while the other two peaks are scaled proportionally. In this way you get visual information on relative peak intensities. However, sometimes the final scaling ratios cannot be predicted accurately by HT's top graph, and hence you can see differences as in your example. This is quite unusual though. Note that the positions of the red, green and blue peaks after HT match the predicted positions very accurately. So this is not a bug, but a limitation of the histogram prediction routine.