Okay no, I didn't get a 1099-R for those accounts. Sorry, I misspoke. I should have said forms 5498 which list RMDs required for the next year. I guess that's the main issue here - TurboTax does not ask about forms 5498 and I am unable to even open up a 5498 form.
I had been telling TurboTax that all of an IRAs distributions were for the RMD but then I thought maybe the problem was that the excess was not able to roll over to other IRAs. So I entered that only a part of the distribution, the required amount, was for that RMD, hoping that the excess would be applied to other accounts. Well, that didn't work either.
I haven't found a way to convince TurboTax that I don't have a penalty. I am unable to override the penalty by entering 0s in the 5329-T form or even by deleting the form. So TurboTax is basically worthless to me now and I wasted my money on it.
