The program offers you a chance to make adjustments after entering the forms. Make your correction there. My guess is that some question got answered differently than the computer thinks so it limited your credit.
If you add the two 1098 forms together, that is the maximum you can take. Any amounts used for nonqualified mortgage debt must be subtracted out.
Because the mortgage interest is going to a worksheet to make calculations, the adjustment is allowed and goes straight sch A. Another option, just enter one form and put the total allowed up to the total of the two forms as all paid on one form. The form's worksheet does not go into the IRS so your return is not wrong when you make adjustments or change the numbers on forms.
The IRS has a quick quiz to help you determine the deductible amount. See Can I Deduct My Mortgage-Related Expenses?
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