After you file

I wonder if I am entering in the wrong area? I have been going to 'Less Common Income', then 'Sale of Home'. Under 'Sales Information' the box appears with 'Did your receive a Form 1099-S that reported this sale?' I ran through all the steps with the box checked, and I ran through all the steps with the box not checked. In both cases, all the gain was treated as taxable, and the tax due shot up dramatically. So, I must be entering in the wrong place?