The tax return that you filed had a balance do on them and they will always say there was a balance due on them even if you paid the balance due. If you went to a local tax pro and walked out with a paper copy of the return showing a balance due on them then would you expect the paper copies to magically change once you paid the balance due ???
The same thing happens with the TT program ... you may have sent payment directions to the IRS/state (which they complete) with the filing of the return but at no time did TT pay anything for you nor do they get an feedback of the payment being made thus the program bottom line will never change. There is not even a place for the payment on the form 1040 even if they could report the payment. Proof of payment is your cancelled check or online bank/CC/debit card statement.
