It sounds like you're seeing a tax on excess accumulations in your retirement account, even though you've taken all your Required Minimum Distributions (RMDs). Here are a few reasons why this might be happening:
Turbo Tax changed this year. When it asks about the RMD it is only asking for that one 1099R. You need to enter the amount in box 1 on that single 1099R for the RMD, not the total RMD for all. Even if they would add up to more or less. And maybe try leaving the cents off both the 1099R and the RMD questions.