I also had this problem; I did as you said, except I only PARTIALLY rolled over my RMD's back. The Form 1099-R in Turbotax is correctly showing the amount that was rolled over. But the 1040 form is saying that my taxable amount from the distribution is ZERO. It's not picking up the rollover amount from the 1099-R. If I try to override the taxable amount on the 1040 to show the partial rollover, it doesn't give me that option.
I actually called one of the very nice Turbotax CPA's, and she said that the IRS hasn't updated these forms yet; she said that it should be corrected by tax submission time, February 12. Does that sound right?
