I would go and re-do the RMD-related area (1099-Rs) and answer all the questions again (if you haven't already done that). When mine was messed up, it kept coming back with a question about whether I took the remaining RMD within a certain "window" (this was completely irrelevant because I had satisfied my entire RMD so there was nothing further to take), and that's when it would assess the 25% penalty. When it seemed to have been corrected, and when I worked on that section again, it no longer asked that question - it only asked me what my RMD was and exactly how much RMD I had taken. It then recognized it as the correct amount and did not assess the penalty. I don't understand what's going on with yours. If they don't get it corrected for you in a couple weeks' time, maybe you should switch to another tax prep service.
