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Two completely different entities. The US Treasury takes longer. The first page of your tax return PDF is the Filing instructions - that page will show the account and amount you have scheduled. It normally takes the IRS a few days to take the payment, but it is effective the date you scheduled it, and confirmed by your e-file acceptance receipt.
See the IRS FAQ page
this won't help for this year but I use "send a check" option and don't provide any payment instructions via e-file, then just pay directly at irs.gov (which I have to do for Q1 ES anyway), IRS usually debits my account that night so there is no mystery or waiting.
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