TurboTax Having problems Reporting RMDs

Is anybody else having problems with 1099R entries and RMDs? I submitted my taxes in February and got my refund quickly, but when I opened TurboTax a couple of weeks later (after an update), the 'refund' had changed to a 'taxes owed situation. TurboTax marked several 1099R forms as "not finished" (they were "finished" when I filed). A deeper investigation revealed that TT showed that some boxes ("Entire Gross Applies To RMD") were now unchecked (when they had been checked previously). Even when I attempted to fix this, the Form 5329-T just can't be made correctly. I am sure my filing was right, but what is going on?