I had a similar problem. I entered the amount from Box 1 which is the full amount of the distribution I took for that year (this includes the RMD). The question that TT asks with regards to the RMD specifies that if you took it out by April 1st, you do not need to enter the amount of the RMD. I think what it is doing if you enter the amount, is to calculate the penalty and tax on it.
When I entered zero - it removed the penalty and tax it had created for the amount of the RMD.
If you withdrew your RMD within the time period allowed - do not enter an amount on the question about RMD's.
