TurboTax does not and cannot update your account showing the amount is paid. There is no link between the IRS and TurboTax for payments made. As long as you have paid the taxes owed you don't have to worry about what TurboTax tax monitor is showing, it will not be affect your 2016 tax return.
If you have overpaid, the IRS should catch the overpayment and send you a check for the amount overpaid.
