How did you pay the estimate on April 8? Did you send in a check or pay online at the IRS? If you mailed a check did you send it with a 2024 1040ES slip or with a 2023 extension? Sounds like they applied it to 2023 as an extension or tax due payment.
If the IRS added it on to your 2023 return and you got it back then forget about it going forward. If you want to pay an estimate for 2024 you need to send it in again with the right 1040ES slip or add it to the June payment.
Or you can pay on the IRS website. Be sure to pick 2024 1040ES payment
https://www.irs.gov/payments
