This is not a TurboTax problem. You must enter the Form 1099-R exactly as received, including the amount shown in box 2a of the Form 1099-R provided by the payer. You then must mark the box to indicate that the distribution was transferred to charity and the amount that was transferred to charity. TurboTax will include the entire gross amount on line 4a but will exclude from line 4b with the "QCD" notation the amount transferred to charity.
