After you file

Well don't do anything in the program until the IRS has fully processed your return and the original refund has been recieved.  Only then should you start the amendment process.  When you do review the 1099-R input screen ... did you accidentally enter the amount in box 1 in box 2a when the box should have been left blank ?  If you did then you probably told the program it was correct thus overriding the program's calculation of the code G.    Did you enter  code G in box 7 ?