For the code-2 Form 1099-R reporting the conversion from the traditional IRA to the Roth IRA, make sure that the IRA/SEP/SIMPLE box is marked. If it's not marked, TurboTax will treat it as a rollover from the 401(k) and not populate Form 8606 Part II. That Form 1099-R should also have box 2a equal to box 1 and box 2b Taxable amount not determined marked. (If the form provided by the payer is not prepared this way, it would seem to imply that the distribution came from an account that was not an IRA.)
