I am a volunteer for the AARP Tax Aide program. In 2022 (for 2021 taxes), a client filed a 1040-X because he received a 1099-DIV after we had filed his original return. He paid additional tax because of this, but the IRS sent him a letter that he hadn't paid enough. It didn't explain why, and we were dumfounded.
Turns out the late 1099-DIV contained Qualified Dividends and Capital Gains distributions. The software correctly used the QDCG worksheet, but the IRS used the straight Tax Table on all of the the additional AGI on the 1040-X, thus overstating the amount owed.
I am not sure whether the taxpayer sent in a copy of the late 1099-DIV showing the QD and CG. He's tried to get an understanding from the IRS, but all they'll say is that he owes.
Should we seek help from the Taxpayer Advocate, continue trying to find someone at the regular number to help us, or something else?