Do you have bank/credit card statements that show that you paid your tax due? TurboTax never knows how, when or even if you paid your tax due. Your only proof that you paid will be your own bank/credit card records.
We just got the same letter in the mail today, but our bank account shows that our tax payment was debited out when we filed. We used the direct debit option. I'm going to have to try calling the IRS on Tuesday I guess since they aren't open before then and try to get through and figure out what's going on, unless TURBOTAX has an answer for us!