Box 3 on Form 1099-INT is used to report interest on US Savings Bonds and treasury obligations. Any amount reported in box 3 will be added to amounts reported in box 1. Then the total will show up on your Schedule B. You should not include the box 3 amount in box 1 as well.
Without knowing the details of your other income and deductions, there is not enough information to comment about whether your bottom line income tax should have changed when you entered the interest income.
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