After you enter the 1099-R, you will need to continue to answer the follow up questions in the section. You will be entering your previous years Roth IRA conversion (basis). After you complete this information, the amount should not be taxable.
You can verify by selecting (online versions) Tax Tools, Tools, then View my Tax Summary. Then select Preview my 1040 on the left black panel. The IRA distribution should be reported on line 15a and the taxable amount of 0 on line 15b.
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