Jim,
While it's been a long time since I have done any extract brews (except for the occasional adding of LME to my wort (AllGrain) to get the OG up..... I used to do exactly as you describe abobe .. but for 5 gal.
Anyway, question 1 - I believe that you should choose "PARTIAL MASH" instead of "Extract". But as stated , it has been quite a while.
Second question- I don't understand it either, I have seen the same anomolie ( at least with the FG) but I just live with it. I do find, however, that BS's calculations seem to be nearly dead on with the actual beer that I am brewing.
I can't help but wonder if the new version of BeerSmith we are all waiting for might adress this issue. It may be a "attenuation" issue, or something like that. But for now, I would say brew, and then compare your actual numbers to BeerSmith's and sii if it isn't real close. There are lots of little variables that can pop up during brewing, so I just trust the calcs and have never been dissappointed. The beer is ALWAYS good!
Welcome to a GREAT hobby!