It almost looks like you had an efficiency factor baked in during the calculation. When you use extract/sugar, the efficiency is 100% -- the gravity points go straight in to the wort. When you mash, you get less than the theoretical maximum (unless you're Dave Miller, but that's a joke from the '90s).
Dry malt extract and sugar should give you about 45 points per pound (my recipe calculator says 43 and 42, but 45 is close enough; liquid extract is around 36 points).
So just add up the pounds of extract and sugar, multiply by 45, then divide by the batch size. That should give you your gravity target.
When you mash, you do the same thing except you scale the points from the grains by your brewhouse efficiency (typically 70-75%, but it varies). If you were expecting a much lower gravity, it makes it sound like the calculator had some efficiency factor baked in. Or that you accidentally told it you were using liquid malt extract instead of dry. I'd bet that it's one or the other rather than a broken program.