Sometimes banks have more than one routing number. If your bank has several use the one for electronic transfers. You may want to contact your financial institution as they may have changed their procedures recently.
Also, if your bank is Bank of America, some Bank of America customers have discovered that the routing number printed on their checks are not being accepted by the bank for direct deposit of refunds or for direct debit of taxes owed.
Here is a TurboTax FAQ for more information:
Please see this for general information on bank routing numbers and how to properly enter the information:
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