You may not have enough deductions before or after entering the points so the deduction remains constant as the standard deduction.
When you tried entering the points under 'points not on 1098' section, did you also report points reported on 1098. That would double the amount of points and make the deduction go up.
If you do have enough deductions try this: Enter the 1098s in order received. Mark the first one 'Not the latest 1098'. When you get to the 'Points' page, select both 'This is a new loan in which I paid points' and 'I bought or improved my home with this loan'. On the second 1098, select 'This is the latest 1098'.
