I can't comment on why the calculations are different. It may be the estimation of fermentability of the sugars or DME that are used. I use the BeerSmith calculator and found early on that my beers were a bit over-carbonated. So now that I have a correlation, I specify a slightly lower carbonation target and everything works well.
As with most models and calculators, you can go crazy trying to parse them all out to figure out the differences. Pick a model and use your results and experiences to figure out where the outcome matches your expectations.