Just thinking out loud. So you made 2 payments on April 15, 2024? One for the 2023 Extension $7,147 and a 2024 $5,000 $2,500 Estimated payment?
When did you file 2023? Did you have a refund for 2023? Did you manually enter the extension payment into your 2023 return? Maybe it was already listed from April and got in twice? Open 2023 program and see if you have any refund applied to 2024. I would look all though everything in Forms mode and see if the 7,147 shows up anywhere else it shouldn't be.
Also start a new 2024 return and transfer from 2023 again. Don't enter anything and see if it shows up in 2024 wrong again and all the amounts from 2023 are right. First thing, better save this return with a name you can tell apart from your real 2024 return and you don't overwrite 2024. Go to File-Save As.
