No matter what the ingredient, there will be some contribution to volume. From what I can see, BeerSmith does not make any corrections for this so you'd just have to manually subtract the difference.
There are a few places within the program where you can compensate for volume, play around with some of the variables such as Trub Loss and Batch Size and watch carefully what each does - you'll come up with a fix that suits your needs.
Remember, the software is only a tool - it isn't expected to be perfect for every situation. If it doesn't do exactly what you want it to do, there are always work-arounds.
