The 'This loan was paid off' box should not be selected. I ran some examples on my desktop version and it deducted all interest and points I entered (my example had a balance less than $750K). I entered the first 1098 as I suggested before with both boxes selected and 'not the latest 1098'. I entered the points on the 1098 and made sure the 'paid off' box was not checked.
For the second 1098, I selected 'is the latest 1098' and left all boxes unchecked on the points info page (although I think it would be okay to check the 'Bought this home' box (2nd box from top).
A couple of things to check if you still think there is a problem. First, check the interest and points reported on Schedule A line 8a. Remember, your interest and points will be limited because your mortgage is over $750K. If that doesn't work, delete your mortgage 1098 and reenter from scratch. With all the different things you have trying, there may be some leftover junk giving problems.
