Beersmith calculates IBU contributions to the recipe on a per-ingredient basis. It has to assume that you don't whirlpool the boil additions (after all, you might not whirlpool), and when calculating flame out additions, it can't know how long it takes you to cool the wort, so it has to assume zero time (pretty accurate if you have a good CFC or plate chiller and start running off wort immediately through it into the fermentor).
The whirlpool calculation is a recent addition that calculates the IBU from each whirlpool/hopstand addition. Since the calculation is done on a per-ingredient basis, it doesn't include hops previously added to the wort in the calculation. Obviously, hops that are boiled for any length of time before being whirlpooled can't be calculated as a simple whirlpool addition (because they've already given up a lot of their bitterness), but whirlpooling them will increase the IBUs extracted.
So you've got a couple of options if you want your process to more accurately follow the Beersmith model in order to hit the IBU numbers: Remove your boil hops at flameout, and/or move your flameout hops to the whirlpool (and/or calculate them as such). Remember though, IBU calculations are somewhat inaccurate generally (particularly for late additions?), and there's a couple of different formulae you can choose between.