If you are looking at the summary screen it only shows the gross distributions and not the taxable portions ... on the return only the taxable portion will be on line 4a.  Switch to the FORMS mode and review the actual forms.

Line 4B on the IRS form is designated as the taxable portion of IRA's rather than Line 4A which is the TOTAL of IRA's.  Rather than Line 4A, Line 4B should then be the taxable amount which is the LOWER AMOUNT of the two lines if one of the distributed IRA's is a ROTH IRA which is not taxed.  Is this not an error in Turbo-Tax - the wrong boxes are being populated for taxable portion of IRA distributions and total IRS distributions?

Sounds like what you said is right.  Are you saying line 4b has the wrong taxable amount?  Forget what line 4a has.  There are situations where 4a can be less than 4b.  

The combination of the old lines 15 & 16 to the new line 4 has had messy results ... ignore line 4a  and just concentrate on line 4b ... if the taxable portion is not correct then review the 1099-R entry screens for accuracy and the follow up screens in that section to make sure you indicated it was not a taxable situation.