I recommend reviewing the input and comparing it to your 1099-R to confirm all of the codes and boxes match what is reflected on the form.
It sounds like a different code may have been entered into the program. If one question is answered slightly differently, it will go through a different series of questions to ensure the retirement distribution is taxed correctly.
If you are still having issues, I would delete that particular 1099-R form and re-enter it.
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