I think I know where you may have gone wrong in the estimator tool:
Education expenses can be deducted on schedule A as an itemized deduction, but interest on student loans (from previous year's expenses) is an Adjustment to income.
Its fairly common for people to mix up adjustments with deductions because they have a lot of similarities. Both of them will reduce your taxable income which saves you a bit of tax (based on your marginal tax rate).
But the big difference is that "Adjustments" can always be claimed, but "deductions" are only beneficial if your total deductions add up to more than your standard deduction.
In 2017 your standard deduction as a married couple will be $12,700. If you have an "adjustment" for $1000 you can take that on top of the standard deduction for $13,700 total. But a $1,000 "deduction" is worthless because you'd have to give up the $12k in order to claim the $1k.
Anyway, I think what you did is you entered your student loan interest into the section for itemized deductions. You should double check to make sure you are entering that into the "adjustments to income" section and you will be able to claim it.