According to the Tool-Tip Text for the Batch Size field it is "as measured into the fermenter" and in another location "Actual Volume in the Fermenter", which I take to mean how much liquid you put in the fermenter before it starts fermenting.
The issue is that the calculation of required water takes into account the Trub Loss value to produce the water levels needed to meet this size.
For example, I like to put 5.5 gallons into my fermenter, so I set batch size to 5.5. Beersmith v1 used to tell me a pre-boil volume of 6.87 (which is pretty accurate) and beersmith v2 tells me 7.89 gallons by default. The discrepancy is because it accounts for trub loss to early in the process. When I set the trub loss value to 0 beersmith v2 outputs a more correct pre-boil volume of 6.85.
The issue is that the calculation of required water takes into account the Trub Loss value to produce the water levels needed to meet this size.
For example, I like to put 5.5 gallons into my fermenter, so I set batch size to 5.5. Beersmith v1 used to tell me a pre-boil volume of 6.87 (which is pretty accurate) and beersmith v2 tells me 7.89 gallons by default. The discrepancy is because it accounts for trub loss to early in the process. When I set the trub loss value to 0 beersmith v2 outputs a more correct pre-boil volume of 6.85.