This may be my bad.
In testing, I do all sorts of things, which I don't necessarily remember. Shame on me for giving you the full story (as I remember it).
Do this...
1. write down (if you don't have a paper copy) the 1099-R that we are talking about.
2. Delete this 1099-R (either in Forms mode or in Step-by-Step)
3. Check Forms, and see if the 5329-T had gone away (I don't think it will yet).
4. Since you are already in Forms mode, delete the 5329-T.
5. Save your tax return.
6. Reopen your tax return.
7. Re-add your 1099-R
8, Now see if your 5329-T is gone.
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