If I enter a 1099R that's NOT an IRA....it calculates correctly.   If I enter one that has the IRA box checked it doesn't tax it at all.   Note:  I didn't check the ROTH IRA box....but, the regular IRA box.  I hope that helps you figure it out.  I have tried my best to relay this info to Intuit but, they don't see it as a problem.