I don't think it had anything to do with how I entered the 1099-Rs. The difference seemed to hinge on how I answered the questions about how much of the withdrawal applied to the RMD: 1) all of it; 2) some of it; 3) none of it. I settled on #1 since that seems to keep things happy. My withdrawal was about 2X the RMD so I had initially picked #2 since that seems more correct to me -- only some of the withdrawal was necessary to cover the RMD -- but after the recent software update that generated a significant penalty. Switching to #1 put me back to where I was before the software update. I think I last updated a week or two ago so it was a fairly recent change that even alerted me to an issue. (I always worry about this type of thing should I end up filing before some critical update has been released for the software. I guess I'm "fortunate" to still be waiting on a 1099.)
