I tried a manual calculation with a 2020 return and came up with similar to Lacerte. However, with complexity of the tax calculation on these particular returns, I cannot be 100% sure its correct or whether its the IRS or Lacerte.

Comparing IRS transcripts, capital gains tax calculations are identical. But, the overall tax using schedule J is different. The transcripts do not provide line 4 of sch j which is where I'm guessing the difference must lie unless the averaged tax using prior year rates is wrong (which the transcripts indicate they are the same as reported on the tax return). Line 4 is a current year tax calculation (capital gains tax worksheets) when using schedule J. Several high income tax returns between 2019-2021 have had this issue. Odd that the IRS and Lacerte agree on the 'normal' capital gains tax calculations but not the capital gains tax calculation when involving Sch j...if this is the issue.

I appreciate the response and will be manually calculating the tax on a 2021 return which I had just received the notice. And, will compare the worksheets between the IRS and lacerte.

I really hope to see if there are any others out there that may have experienced it. Prior to 2019, Ive never had issues. Im probably about 80% Ag returns so its odd to have this pop up in recent years when I've filed so many similar returns over the years. I know in 18 or 19, there was a 1250 recap issue the IRS had changed due to worksheet errors but it doesnt seem to be the issue.

To be continued once I find time to go through a 21 return manually. I just hope if someone else has seen this issue to mention it here. I brought up a Lacerte 2021 issue with a state tax return and Lacerte was great to research and fixed the software quickly in the heat of tax season. This issue seems to not get the investigatimg I was hoping and why Im mentioning it here to see if there are others. There have been some substantial dollar differences.

Thanks again for the response.