TurboTax is incapable of directly handling a single code G Form 1099-R that reports distributions to multiple destination accounts of differing types. You must split the Form 1099-R into two, one for the portion rolled over to the traditional IRA and the other for the portion that was the In-plan Roth Rollover (IRR).
Note that IRS Notice 2014-54 only allows the box 5 amount to be allocated entirely to the IRR (or any other allocation you choose) if the direct rollover to the traditional IRA and the IRR were requested to be made at the same time. If these were two separately requested distributions from the traditional 401(k) account (which probably is not the case here), each would generally receive a proportionate share of the box 5 amount.
[Edit] Because the amount in box 2a is zero, you probably will get the same result by indicating that the entire distribution was rolled over to a Roth 401(k) even though only a portion of the gross amount appears in box 5. The question that TurboTax keeps defaulting to No is one for which TurboTax does not record the answer, so TurboTax simply asks it again. As long a the correct ($0) taxable amount appears on Form 1040 line 4d, it's being handled correctly.
