Unfortunately, you will have no choice but to go ahead and re-pay the tax bill with the interest. If they added additional penalty amounts due to the late payment, then under the circumstances you could request that those penalties be waived, since it is not your fault that the payment was not accepted to begin with.
I know it is very frustrating to have something like this occur, but unfortunately the IRS makes mistakes just like anyone else, and actually they make mistakes of this nature all too often.
I just had a similar experience on a tax return for my son where I filed an amended return
for him which resulted in a small refund being due. Instead of issuing the refund they sent him a bill for $258 plus interest and penalties. After lengthy conversations with several IRS representatives, it was just determined that apparently two different representatives were working on the return at the same time, and the figures ended up being posted incorrectly.
We tend to think that mistakes like this cannot happen with the IRS, but they happen more frequently than you might expect. But the botXXXXX XXXXXne is that it does not take away the liability to pay the taxes, even though they made an error.
You should not, however, have to pay any additional penalties they may have assessed as a result of this error. Interest charges are something they will never waive, but there should be no additional penalties assessed to you. I would deduct any additional penalties that were included in the payment request, and attach a letter of explanation.
You should be safe to go ahead and just mail the payment with the notice that you received, as chances are the same error will not occur again. But you might want to include a brief letter with your payment explaining that this is your second attempt to pay this bill, and that your first payment was returned in error. That way the representative who receives your correspondence can look back on the history of your account if they have any doubts as to the tax you owe.
If this was helpful please press the Accept button. Thank you Brock, and let me know if you have more questions.
I am happy to help you with whatever I can, as I realize how frustrating this can be.