Late extract edition and IBU calculation

I just put an all extract version of Jamil's Evil Twin into the fermentor this morning which uses all late hop additions for the bittering and aroma.  I adjusted his all grain recipe with Beer Smith and went with half the extract at 60 min and the remainder at 30.  As I was brewing, I began to think "why did the IBU's change in Beer Smith when the first Hop addition isn't until 10 minutes after the late addition of extract"? There is about a 5 IBU difference between the late addition or having all the extract at the beginning of the boil.

Does the extract require some time between the addition and when it effects the hop utilization? Or is this a miscalculation because normally the hops would be in for the full boil?

Two things to verify are the Hops Utilization model under Tools \ Options \ Bitterness, and a check mark for late addition extract in that extract's ingredient window. 

JZ uses Rager, and BSmith defaults with Tinseth, so make sure you're pegging against Rager at first. 

Thanks for the Rager/Tinseth option... totally missed that when I calculated how many hops to add and when.  It would seem I got lucky on that one as the two calculate pretty close in this case (25.1 vs 25.7). 

I double checked the 30 min late addition check box.  And sure enough, the IBU's change about 5 points when the malt is put in at the beginning versus at the 30 minute mark.  I only found it odd because the hops aren't in the boil at either 60 minute or 30 minute so I would think (key word there) that the utilization would be the same because either way the specific gravity should be about the same when the hops go in (20 minutes for first hop addition).

There must be more going on there than just gravity effecting things.