What is the code in box 1 of the 1099-R you received for the "withdrawal" from the traditional 401(k)?
Also, was this a trustee-to-trustee transfer? If it wasn't, then the plan administrator was required by law to withhold taxes from the distribution, and it's up to you to "make up the difference" for this to be a 100% rollover.

I originally pulled this 1099R document from the vendor into TurboTax through TurboTax. I went through the form again. Even when it said "0.00" on the 1099R, I deleted the autofilled "0.00" and left it blank in TurboTax. This almost immediately adjusted the Federal Tax due back down and showed on a later screen that the amount is no longer taxable.

@jlaufer1 -  What code in box 7?
Is the zero in box 2a?

Box 2a was "0.00". Code in Box 7 is "G". All of the information and questions were entered/answered correctly into TurboTax. TurboTax was somehow reading the "0.00" entries in a weird way. By removing those "0.00" entries, it corrected the amount of tax due. My problem was solved. Thank you.

I am pleased that your problem has been solved.

@jlaufer1 - Unfortunately, that does not "solve" the problem, but creates a new one.

A 401(k) distribution 1099-R with a code G and a zero on box 2a, indicates a direct rollover to a *Traditional* IRA, not a Roth IRA.

The IRS receives a copy of the 1099-R form the payer and what you report must match that 1099-R.  The IRS also receives a 5498 for from the receiving IRA custodian and expects to find a Traditional IRA deposit, not a Roth.

If you instructed the 401(k) custodian to roll this to a Roth IRA then box 2a should have had the same amount as box 1.   If that is the case then the 401(k) trustee needs to issue a corrected 1099-R.

If, *you* changed the IRA account type on your own to a Roth, then you need to delete the 1099-R and use a substitute 1099-R (last choice on the 1099-R type screen) with the same information as the original 1099-R except box 2a would be the same amount as box 1 (unless there is a box 5 amount, then box 2a would be box 1 minus box 5).    You would select the interview choice that the distribution was rolled to a Roth IRA.

The substitute will ask for an explanation statement where you state that the 401(k) was actually converted to a Roth IRA rather then being rolled to a Traditional IRA.  Without the substitute 1099-R and the explanation statement you will probably be receiving letters form the IRS in about a year or so when they match the forms.

@macuser_22 I appreciate you trying to help, but you’re trying to solve a problem where you don’t have the whole picture. Your response may help someone else here, so thanks for contributing!

I rolled this over from one company to another. I then converted with the 2nd company, who then supplied a separate 1099R which I had uploaded and the correct amounts and codes are shown on the form.

There should be no need to change the box 2a amount then.  You said you removed the zero from box 2a.  The 401(k) to 401(k) rollover code G *requires* a zero in box 2a and it is not taxable.   The 401(k) to Roth conversion *require* the taxable amount in box 2a.   

It might have been a subsiquent question Turbo asked me after I initially deleted the “0.00”s. So I’m sure if it was required and they asked, that is exactly what happened. I then put “0” when asked.

OK good.   As long as the forms were correct, no problem then.