Don't go thru it again. It's marked as such when you go all the way thru and re-marked it properly, adn stays tha way unless you go thru it again.
Why doesn't it "keep" during subsequent run-thru's....don't know, but many times the software can't know why you are going thru the Q&A again, so it starts all over....IF...you run thru that 1099-R again.