This might be considered a work around, but it works. Assumption - that your total RMDs taken were in fact the amount you were required to take.
After entering your 1st 1099-R, in the following questions enter the amount from the 1099-R as the RMD taken (regardless of what you should have taken from that particular IRA) then select entire distribution was applied to your RMD. Then with your 2nd 1099-R, enter the amount taken as an RMD taken, then select entire distribution applied to RMD.
You will not trigger the need for the penalty form. TurboTax does not know how much should have been taken out of each IRA, you tell it that with the follow-on questions. If you tell Turbo Tax what RMD was for each IRA and that the entire amount was applied to RMD, Turbo Tax is happy.
