Get your taxes done using TurboTax

Yes. This usually happens when the software gets caught between the amount set by Empower and its own way of checking the numbers for direct rollovers or after-tax contributions. To alleviate this, I recommend doing the following.

1. Delete the Form Entirely: Go to Tax Tools > Tools > Delete a form. Find the 1099-R from Empower and delete it. 
2. Manual Entry (Do not Import): Go back to the 1099-R section and choose to type it in yourself.
3. On the entry screen, ensure that Box 2b "Taxable amount not determined" is NOT checked. If that box is checked, TurboTax is programmed to ignore Box 2a and calculate the taxability itself.
4. After you enter the boxes, TurboTax will ask a series of questions.
5. If this was a rollover to a Roth account (where the earnings in Box 2a are taxable but the contributions in Box 5 are not), answer the questions carefully.

•  Look for a screen that asks if the amount in Box 2a is the correct taxable amount. This will be yes or no

If the summary still shows double-counting after a clean entry, many users have successfully bypassed this by "splitting" the 1099-R into two entries in TurboTax.

• Entry A: Report the taxable portion. Enter Box 1 and Box 2a as the same amount (the taxable amount). Leave Box 5 blank.
• Entry B: Report the non-taxable portion. Enter Box 1 as the after-tax amount (Box 5). Put $0 in Box 2a and enter the after-tax amount in Box 5.

While this looks different than your paper form, the total of Lines 5a and 5b on your 1040 will be perfect. The IRS only gets the final 1040 totals, not the individual TurboTax entry screens.