backdoor Roth tax payment procedure

I made several Tira conversions to Roth in '24.  I made IRS "direct payments" online to cover my anticipated taxes on the conversions.  This totaled a 6 figure payment and were listed in TTax  "Tax Payments Worksheet", Lines 18b & 18c.  These payments were made at the time of the conversion.  The payment is reported on the 1040 line 25c as a withholding.

 

The mutual fund company did not give me any tax forms for these transactions.  I have reported the conversions on the 8606-T (and S). 

 

My problem is that the IRS sent me a check for the 6 figure amount as an 'overpayment'.  I marked this check void and returned it with a letter of explanation that it was for tax on the conversion.

 

The IRS replied to my letter saying in part "Our system shows tax of X and withholding of Y".  The amounts X and Y are correct and listed on my 1040 line 24 and 25d.  The letter further states "We received two payments of 'A' & 'B' on <Date, 2024>."  A & B match the numbers reported above on lines 18b & 18c.  And they sent a new 6 figure check as a refund.

 

IMO They seem to be confusing withholding with direct payment.  Perhaps I did not place the direct payment numbers in the correct spot on my return.  Whatever the case it appears I will get nowhere returning the 6 figure check again.  I'd love to keep it but I would not love being discovered and explaining this stuff.

 

I tried calling them when I received the first check and after 6 hrs of getting no where not getting someone to help me I gave up.  

 

If there is a glaring error in reporting with the info I gave, I will file an amended return.  Assuming TTax put the numbers in the right spot, I am looking for advice on how to correct this apparent error on the part of the IRS.