We can't see your tax return, so this is just a guess. The long-term gain increases your Adjusted Gross Income (AGI), regardless of what tax rate is applied to it. The increase in AGI could be reducing some deduction or credit that is not directly related to capital gain or loss. Try comparing Form 1040 line by line before and after entering the gain, to see what else changes. Depending on what changes on Form 1040, you might then have to look at a schedule that the changed amount comes from.
