@emcrobbie I don't know if you have contacted support or if you resolved this problem, but I ran across an old forum post from a couple of years ago that might have the solution. 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 reduce your Federal Tax Due.
Please let us know if this solves the problem.
