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I am not sure what might have changed between the two version which have caused this change. Normally if you have imported your profiles, they should remain consistent between the two versions.
It sounds like you need to revisit your equipment profile to account for your volume balance. Places to look are your boil off rate, process losses, mash tun losses, and grain absorption. If you have good measurements and notes from your previous brews using BS3, then you should be able to go back and recalculate these figures compared to what you have in your equipment profile (or grain absorption which is a universal attribute) and make adjustments to get the program to match your actual figures.