I'm not understanding the problem. Turbo Tax will always say the final tax due or refund. That's just the state of your return when you filed. They don't know it got paid. It isn't updated when you pay or get a refund. Your only proof if your bank account or credit card showing the payment coming out.
Are you using the Desktop program? What filing history? Where? I think there is some problem with the Desktop program Check Electronic Filing not being updated with the accepted status. If you got the refund or your payment went though then don't worry about it.
