The Mr Malty calculator is based (I think) on dumping the entire contents of the starter flask into the wort.
If you decant off the liquid and only pitch the slurry, you will have less yeast. Also - I think the calculator assumes 18 hours? What if its more or less?
Its probably not a big deal if Im off a bit, I would hate to over pitch yeast though, and not get a good flavor.