I am seeing the same/similar problem. I have two 1099-R forms. Both are from rollovers from 401(k) to an IRA, all of the funds were rolled over. One has a Gross Distribution amount, box 2a Taxable amount is 0.0, Check Box 2b Total Distribution is selected, and Box 7 is G-Direct rollover. The other 1099-R has a Gross Distribution amount, Box 2a has a Taxable amount (to effect a change of basis), Box 6 has a Net unrealized appreciation amount, and Box 7 is 7-Simple distribution.
The 1099R Summary form shows Gross (on Line 22) that is correctly the sum from the two 1099-R forms. Line 25 lists that same amount. Line 26 incorrectly lists Taxable amount in box 2a as the sum of the Gross distribution value from the first 1099-R form and the Taxable amount from the second 1099-R form (rather than the sum of the Taxable amounts listed in box 2a of the 1099-R forms). But then the Taxable amount transferred to Form 1040, line 5b, listed on line 32d is 0.00. Line 5a of Form 1040 shows the sum of Box 1 from the two 1099-R forms (as expected), but Line 5b of Form 1040 shows 0.00 (I expected to see the Taxable amount from box 2a of the 1099-R form). As a result, TurboTax is calculating the taxes incorrectly because it isn't including that Taxable amount. Note that after inputting the 1099-R there is a question 'What did you do with the money from Company X?'. If I select the option that I moved the money to another retirement account (which is what I did), the errors described above occur; if I select the option that I 'did something else (cashed out, etc.)' - which is not what I did with the money, the errors described above go away, and I appear to get the correct results. But I don't have a high degree of confidence in the results, because it seems that if I answer that question correctly I get wrong results, but if I answer it incorrectly I appear to get correct results.
