Since a QCD can only come from otherwise taxable amounts, there is no change in your basis in traditional IRA contributions from making a QCD. If your the transfer to the charity is more than the amount of pre-tax money in your traditional IRAs, report as QCD only the amount that is pre-tax and take a charitable deduction for the portion that comes from basis and leaves only basis in your traditional IRAs.
Since you apparently had some pre-tax money in your traditional IRAs, TurboTax reducing your basis by the amount that was transferred to charity means that you have not told TurboTax your year-end balance in traditional IRAs. Click the Continue button on the Your 1099-R Entries page in the CD/download version or the Review You 1099-R Items page in online TurboTax to reach the page that asks for your year-end balance.
