This is because the program uses Brewhouse Efficiency to determine the gravity readings. It applies this efficiency to the total available sugars from the grain bill entered. This determines the end of boil gravity. It then works backwards to calculate your pre-boil/post mash gravity reading. Since you changed the amount of water which was boiled off (loss of volume being a function of time of boil), this means that the volume change dictates the beginning volume while the amount of sugar remains a constant. If you, as an example, have a profile with a 90 minute boil time, the volume is higher for the pre-boil than if you changed the boil time to 45 minutes. The amount of sugars remains the same, so the expected gravity reading post mash would be higher for the 45 minute boil time than the 90 minute boil time.