Posted this over at HBT.. hoping to get an answer. My Pre-Boil gravity is always low and my final gravity is usually spot on. Turns out my Boil off rate was too low and the trub loss to high, so it sorta worked out.
If you create a recipe and go the "vols" tab, then adjust the "trub loss" under "boil and fermentation" the program adjusts the water volume going in, but not the OG of the pre boil wort.
In other words for a normal recipe if it says that your pre boil OG (7.9 Gals) is 1.045... if you were to change the trub loss to say 2 gallons it would adjust the pre boil volume but then the pre boil OG would go up.... despite being diluted with an extra 2 gallons of water.