A Roth conversion is defined as a distribution from the traditional IRA and a conversion contribution to the Roth IRA. The Form 5498 should show the conversion contribution in box 3, not a regular contribution in box 1 and will match up properly with the distribution reported on the Form 1099-R. Enter this in TurboTax only by entering the Form 1099-R and indicating that you converted the money to Roth. Do not enter anything regarding this under Deductions & Credits.
