Double check the ordinary dividend and qualified dividend entries in the 1099-DIV section of TurboTax. You are correct that all of your qualified dividend entries made in the software should flow to line 9b on your 1040 tax return. If you are unable to locate the error, then try deleting the 1099-DIV entries and re-enter the information again.
See the TurboTax FAQ below for steps on how to delete a form. Click "See entire answer" for the full page view.