The question about any portion of a 1099R being a charitable contribution is hidden in a string of questions that appear after the first time you enter all the pertinent info about that particular 1099R and enter all of the amounts associated with it. A page comes up with a list of 10 questions all in a row and the 7th one is the following:
I transferred all or part of this entry direct to a charity.
You need to check that box and then a question will appear as to what portion of the 1099 amount went to charity. At least that's how I finally got it in there.
If you don't check it on that initial entry, you need to delete the entire 1099R and reenter it to get that prompt to appear.
