Here are three possible solutions to the problem. Please let us know if one of these suggestions fixes the problem.
(1) Since you are using the CD/Download TurboTax software, go to forms mode and open Form 4868. Below your name and address there is a box with the heading "Important Information." In that box there is a checkbox A. If that box is not checked, click it to check it. See if that makes your extension payment flow to Schedule 5 and update the total taxes paid.
(2) Open the Tax Payments Worksheet in forms mode and enter the payment with the extension in the Federal column on line 9.
(3) Delete Form 4868, then enter the payment again. Save a copy of Form 4868 before you delete it.
