When you say your bitterness calculations are identical, are you referring to the settings in Options > Bitterness?
BS3 offers some more flexibility than BS2. As it's been updated, some of the calculations reflect significant changes in brewer techniques that result in more IBUs. Just as in BS2, there isn't an upper limit for calculations, even though as a practical matter, there is.
Check the hop type is matched, as well. In BS3, some of the hop types revert to leaf when imported.
In the equipment profile, make sure the large batch utilization and that the WP time is correct, plus the utilization box is set.
Starting with a recipe that has fewer additions, set the large batch utilization to whatever value gives tou the correct IBU for the BS2 version. That should be a baseline to get the other recipes to line up.