There are a number of things that will cause a difference in IBU between a recipe which is printed and how the calculations come out in the software.
First, there are a number of different models for the estimation of IBU. If you are using BeerSmith as it came the default IBU model is Tinseth. The software also gives you the options of using Garetz or Rager. Each of these will give you different values. I am not sure what calculation the Brewer's Best kits use for their published IBU, so that may be one significant difference.
Next, hops are an agricultural product and the amount of the bittering components can (and do) change from year to year, lot to lot, grower to grower, field to field, beginning of picking period to end of picking period. Even within a lot of hops, the % alpha acids can vary greatly. The %AA for your particular lot of hops may vary from the standard used in the recipe calculations made by Brewers Best. Since they are producing and boxing a number of kits at one time and not necessarily using the same hop lot or bale to package from, they most likely use a typical average for the hops they use for a particular recipe.
Third, your process has its own peculiarities in terms of losses and efficiency. If your process has significant losses (or no losses) post boil, this can affect the amount of IBU which make it through the system into the fermenter.
Lastly, the issue I have with IBU is that it is the estimation of tested value which has a rough correlation with the perception of bitterness. The test also does not include other components which contribute to bitterness perception in beer, so in its own use it is an imperfect measure of bitterness. Unfortunately, it is the only metric we have to estimate the bittering perception in a beer. Even then, it is difficult for most brewers to distinguish between two beers that are less than 5 (some say greater than that) IBU difference (as tested).
My advice is to not worry too much about trying to get the kit to match what the software states in terms of bitterness. Brew the kit, taste the beer, enjoy!