The check's in the ether.

The Internal Revenue Service says that it's aware of a delay in processing some electronic payments, and that some taxpayers are receiving notices indicating a balance due even though payments were made on time.
Taxpayers who paid tax reported due on their return electronically may see payments on their accounts as pending, although the IRS has received payment through their banking institution, the agency said.
"The notice may have been initiated before the payment was processed on the account, or the payment may have been processed but contained errors and requires additional handling to address the error before updating the tax account," the IRS said in announcing the delays.
Taxpayers who receive a notice but e-paid the tax they owed in full and on time do not need to respond to the notices. The IRS recommended monitoring the payment activity page in taxpayer's IRS online account, where they will be able to view their payment history as well as pending payments that are being processed. If a taxpayer has checked their online account and does not see the payment processed by July 15, they may call the number on their notice.
Note that any associated penalties and interest will be automatically adjusted when the payment(s) are applied correctly by the IRS.
Taxpayers who paid only part of the tax reported due on their return and cannot fully pay the remaining amount they owe should visit
For affected taxpayers, the IRS apologizes for the inconvenience.