I'm having the exact same problem. The box numbers in TurboTax are not the same as on my 1099R. State income tax withheld has always been line 12 on the 1099R and TurboTax desktop has it as line 14 this year. I've deleted the entire entry and entered it again with the same result. I'm choosing to ingnore the error in TurboTax and enter the numbers where approriate, but TurboTax needs to correct their error.
