@mullerc2
When you filed the extension did you explicitly request the payment to happen ? If you did it can take several days for the IRS to catch up with the pile that was filed on last day.
If you did not request the debit correctly you can make a payment now on the IRS web site to stop the late payment penalties and interest from accruing ... then when you finally file the payment will be accounted for as a payment with extension.
