Hi,
Having just completely rewritten the water profile calculator for the next version of BeerSmith, I can tell you I just checked the numbers again and they are correct within the program. BeerSmith does track the chalk to bicarbonate (which is pretty easy to see if you look at the water profile tool). In fact, the BeerSmith tool lists the chemical symbols for the various water additions making it pretty easy to see how they map into ion contributions.
Also I don't attempt to calculate the residual alkalinity in any of the tools - while some commercial brewers can do this it is hard for a home brewer because they don't often have access to the detailed malt data needed. These numbers vary a lot from maltster to maltster even for comparable malts.
You will be happy to know that I've added an automated calculator to the next version which can, given a target and base water profile, calculate the best combination of water additions to get as close as possible to the target.
Cheers,
Brad