If part of the distribution was before-tax money and went to a Traditional IRA and part was after-tax contributions that went to a Roth IRA then the after-tax amount must be in box 5 on the 1099-R and box 2a must be the same as box 1 but reduced by the amount in box 5. This can only be entered by splitting the 1099-R into two with only the amount that went to the Traditional IRA in box 1 and 2a and zero in box 5 and the amount to went to the Roth in bpx 1 and a zero in box 2a and the same amount in box 5. That is a TurboTax limitation since the money cannot go to two different destinations. Nothing about this splitting to goes to the IRS - they only get the totals on the 1040 form line 5a and 5b.
The 1099-R might be wrong. The amount of after-tax contributions should not be in box 2a which it the taxable amount. If the issuer put what they know is not taxable then the 1099-R is incorrect.
**Disclaimer: This post is for discussion purposes only and is NOT tax advice. The author takes no responsibility for the accuracy of any information in this post.**
