A few other things to consider too.
1. If your state taxes personal income, is the letter from your state and not the IRS? Maybe you paid your federal estimate of taxes to the IRS, yet failed to pay the state or vice-versa.
2. Did the transaction actually go through? If there was insufficient funds on the date of the attempted ACH withdrawal by the taxing authority, the attempt may show up on the bank statement, yet show that it was rejected by the bank/credit union. Typically, the next line on the statement would show a charge for "insufficient funds" or something of the such if your bank/credit union charges a fee for that.
3. Check the bank statement again to see if maybe the withdrawal was "returned" at a later date. I've never seen it, but I've heard of it happening for various reasons I've never understood.
