All charitable contributions from the current year must be deducted within the same category before using any carryover contributions from prior years. When I put in some test numbers in TurboTax, it calculated correctly.
Did your charitable deduction seems to be drawing partially from prior-year contributions of capital gains before deducting the entire current year's capital gains donation? If so, maybe if you delete the prior-year ones and put them back in, it will calculate correctly.
