I have a 401k withdrawal after 59 1/2. Step by step keep reverting back to before 59 1/2 for the 1099R. How can I get that box to stay checked?

You don't.  TurboTax just needs to know the answer temporarily to determine if you have a penalty for an early distribution.  Just mark the correct answer and move on.  Do not edit the Form 1099-R again to determine how TurboTax is handling the distribution, instead look to see that you have no penalty shown on Schedule 2, line 8.