Is 1.079 your actual pre-boil grav? If so, unless your beer is HUGE, then it has to be taking the extract into account.
I ran into this problem when I was doing a Belgian Golden Strong (AG). My pre-boil grav came out low unless you calculated in the sugar and extract (to make up for eff issues) I was using, but the brewsheet clearly indicated you took your pre-boil grav then added the extract & sugar to the boil. My pre-fermentation grav came out right in the end, but I was never sure what was going on (I was battling a drop in eff after changing to my new system which only confused me more).
Does Beersmith have a forum? You might try looking for an answer there.
MATT - 65g in 2k8
3rd Circle Brewery
Ferminatin' - Route 666 Pale Ale
Figurin' to do - Oatmeal Stout, Gueuze, Belgian Blonde, Mild, English Pale Ale, Weizenbock