IRS has acknowledged that, due to increased safety protocols surrounding COVID-19, they are running behind on processing the mail that is piling up in trailers outside their facilities--this includes paper returns, notice responses and especially payments. This problem exists for many state taxing authorities as well. Several of my clients have received notices stating they still have a balance due, even though they mailed a check on time.

This Accounting Today article details the issue and the official IRS guidelines: do not cancel any checks you have mailed to taxing authorities, disregard balance-due notices if you know you have paid, and wait for longer than usual before contacting the IRS about any recently filed returns. They will count payments as being made on the date they received the check, not the date it was cashed, so you will not incur lateness penalties. If you already cancelled an uncashed check, IRS will not charge a fee for the bad check, but do make the payment again as soon as possible.

Paying online is the best way to ensure your payment is processed immediately: here is the IRS payment portal, where you can also pay estimated taxes and installment plans.

Otherwise, for the moment we will just have to wait for IRS to finish processing 2019 returns, and then any erroneous balances due in their records should be corrected. Let me know if you receive any other IRS notice and are unsure what it is regarding.