It has been far too long since my last chemistry class, but I do know that the concepts of pH and buffer solutions are often over-simplified. Activity and pKa probably play a role here in the different observations you see in the simplified models in the lab versus the more complicated mash. http://en.wikipedia.org/wiki/Activity_(chemistry)
Ions are influenced by their surroundings.
Any new water calculator will have to take into consideration the "surroundings", i.e., types of grains used, types of brew salt additions, base water, temperature, etc.