What version of Turbotax are you using? I have Premier. I called the support line today and went through the whole process with him line by line and it was agreed something is not working right, at least in my version. He is escalating this to the tech group and will report back to me in a few days time. I'll post what I find out. Also, he said that changing the 1099-R (by forcing a zero into box 2a) is probably a bad idea as the IRS frowns on changing official documents. You could go to jail...but on the other hand you can die of frustration too.
