Well yes, chalk will not dissolve very much in water, which is why I advocate only adding it to the mash, where the lower pH of 5-6 allows it to dissolve readily.
Dissolving CO2 into the water beforehand to dissolve the chalk will work, but it seems like too much work to me.
Kai, I am at work and don't have your paper available, but are you saying that the pH change when chalk is added to the mash do not match the predicted values? I guess I would not expect them to be perfect but I would expect them to be ballpark.