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The volumes within the program are calculated based upon the amount into the fermentor (batch size) and your process losses. If you know the pre-boil volume to be wrong, then one of your inputs into the equipment file for either process losses (lauter tun losses, loss to trub and chiller, boil off rate, grain absorption) is not correctly entered for your process. You can always use this brew to dial in your losses into BeerSmith by using the amount of water you think is correct and measuring your volumes at each step so that you can calculate your losses and update your equipment profile to better fit your process.