For one thing, when you entered the IRA contribution, you needed to make sure you indicated that it was a non-deductible contribution. You also have to answer the questions correctly regarding the value or basis in your IRA both at the end of the previous and current year.
When you enter the 1099-R form in TurboTax for the rollover of funds to the Roth IRA, you need to first indicate that you moved the money to another retirement account and that you did a combination of rolling over, converting or cashing out the money. Then, enter the amount converted to a ROTH IRA. Later on you need to indicate that you tracked non-deductible contributions to your IRA.
Later in the routine enter the basis (non-deductible contributions) of your traditional IRA at the end of the previous year, and later the value of your traditional IRA at the end of the current year.
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