The difference between the two totals is the amount of interest that you entered. Is it home mortgage interest or investment interest? If it's mortgage interest you might have entered the amount correctly, but answered a question differently which resulted in not allowing the deduction.
In the desktop software go to forms mode and look at Schedule A. Is the interest shown on line 10? If not, go back to the Step-by-Step interview and go through the mortgage interest section again (assuming that the interest your are deducting is mortgage interest). When TurboTax asked whether the loan is secured by a property of yours, did you answer Yes? If the loan is not secured by a home that you own, the interest is not deductible and would be omitted from Schedule A.
