First, it does not matter if you tell the program to add more water than your recipe calls for (ex #2), because the program uses only the water needed for the recipe (5.32 liters) for the pH calculation.
Second, screen shots only show the mash manipulations and no other information for us to go on. What does the water tab look like? Are there any water agent additions? If not, what is the mineral make up of the water?
The calculated pH is cut off of the screen captures, so we can't see what additions are being made. Did you scale them with the change in water volumes or are they flat regardless of the water volume? Same with any acid additions.
The short story is that the pH model is just that... a model. Trust it only as much as it can be verified.