When I enter the 1099R into the program and enter the code Y that is on the 1099R, the program triggers the deduction on the front page of the 1040. Yes the client itemizes a very large amount of charitable deductions on Sch A. This $7600 is not part of the amount going on Sch A. It seems like he was not given good advice by his financial advisor. I am just not going to enter the Code Y.
I'm not too surprised that the software doesn't track this. I suspect at some point in the future it will. In general if ProSeries doesn't do it right, then every TurboTax return filed will also be wrong. The next question is "will the IRS notice?" Time will tell. If the TT users start getting love letters from the IRS and enough of them complain to Intuit then they'll add the worksheet and start carrying over this data.
In the meantime, I might throw together a quick spreadsheet for tracking this each year (if I ever have a client where it applies). IRS Pub 590-B (2025) has an example on PDF pages 14-15 and a "blank" worksheet on PDF page 70 (Appendix D).
Rick