Didn't get much response to this so I emailed Brad Smith. One of the reasons I enjoy using BeerSmith is that Brad is willing to provide great customer service. Here is his response:
If you have a late extract addition, then the individual hop additions will be wrong (they are calculated without taking into account the late extract addition). The total IBUs for the recipe is correct however. I'm looking to correct the individual contributions in a future version.
Note that this only applies to late extract addition recipes - other recipe work just fine and give you the correct numbers in both places.
Beer is proof that God loves us and wants us to be happy.
- Benjamin Franklin (and I don't care if this quote has been largely discredited/misquoted...I like it!)
Beer, if drank with moderation, softens the temper, cheers the spirit and promotes health.
- Thomas Jefferson