How do you know it is Not treating the distribution as a rollover? Are you looking at an income summary screen? That would not accurately reflect a distribution as a rollover.
Is the code in box 7 a G? After entering the Form 1099-R tax data did you indicate that you moved the funds to another tax deferred account?
What is entered on Line 4d of your federal tax return Form 1040? Is the amount from Line 2b of the 1099-R entered on 4d or are the words Rollover shown to the left of Line 4b?
Click on Tax Tools on the left side of the screen. Click on Tools. Click on View Tax Summary. Click on Preview my 1040 on the left side of the screen.
What did you roll it over to? If you converted to a ROTH 401K or IRA Account it is taxable. What code is in box 7? If the took withholding out in 1099R box 4 you had to replace it with your own money when you deposited it into the new account or the withholding will be taxable distribution.
If you are looking at a summary screen or review screen those show the full amount as income and lump a lot of stuff together. You need to check the actual 1040 and make sure it’s right. For 1099R check 1040 line 4b or 4d for any taxable amount. If it was a rollover it should say ROLLOVER by it and 0 taxable.