Hopefully Nutricalc provides some sort of handbook / manual that explains what it is actually calculating?
Shouldn't be anything proprietary that they need to hide, as (a) it really isn't rocket science, and (b) I'd have thought users would want to be able to verify that it complies with labelling requirements.
 
The EU provides a single set of specific conversion factors to be used to calculate energy content - see Annex XIV of Regulation (EU) 1169/2011.
I believe the US uses Energy Value of Foods - basis and derivation, USDA Handbook 74 (attached) as the formal reference.
The two have slightly different factors for some nutrients, and the latter has more specific detail / subtleties in some areas (e.g. different factors for different organic acids, vs. a single value for EU purposes). It's therefore quite plausible that one food would have different labelled energy values for US/EU labelling purposes.
 
The FAO has a discussion piece on it that may be a useful read for you: http://www.fao.org/3...2E/y5022e04.htm
 
Have you tried manually calculating the energy value under the two different regimes, just to check that it agrees with Nutricalc's results?