Retirement tax questions

TurboTax may not know what your RMD is, but it does ask you what your RMD is for the 1099R account you are entering.  If you put it the actual RMD and it is more than the distribution amount, TurboTax decides you owe a penalty and offers to take you to the waiver form, even though I took out more than enough from my other IRA to satisfy the total RMD requirement.  The only way I can figure to get TurboTax to handle this "correctly", i.e. no penalty, is to specify the actual distribution from my second IRA as the total RMD for that account.  TurboTax does not recognize that I took an amount from my other IRA to satisfy the total RMD for both accounts.  In past years, TurboTax handled this situation correctly.  It would be nice if the developers would indicate if this is going to be fixed soon, so we can input the correct information, or if we'll have to file the workarounds we've discovered.