What is changing the refund here is that when this box is checked, TurboTax is giving you two exclusions.
It's excluding the retirement income twice, plus the $5,000 of earned income to which you're entitled under the Retirement Income Exclusion .
This year, because you turned 62, the military retirement exclusion no longer applies, but the "regular" retirement exclusion applies instead.
The prompt is confusing in your case and I will request that we improve that portion of the program based on your input and feedback.
Thank you for sending this additional information - that helped me to see better what the issue was from your point of view.
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