If your Form 1099-R distribution is being taxed, then your basis in the Traditional IRA is incorrect.
In order for the conversion to the Roth IRA to be tax-free, the basis of the Traditional IRA must be at least as much as the amount converted or more. Go back through the IRA Contribution section of your return and be sure that you did choose to make the Traditional IRA contribution non-deductible. The default is to take the deduction and you must read that question carefully.
If your Form 1099-R reported a distribution for more than one year of Traditional IRA contributions, then you need to double-check the prior year basis that you entered for the Traditional IRA to be sure all prior year non-deductible contributions were taken into account.
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