Unfortunately when you do the TT flavor RMD reversal by recharacterizing the transaction as an Indirect Rollover it's going to assume that the amount in Box 1 is to be totally not taxable and 1040 line 4b will be zero. But in your case only the Roth conversion funds should be on line 4b. I tried forcing an Override directly on line 4b but you can't as that amount ultimately originates on the 1099-R even though TT set's it to zero.
I'm grasping here .... create 2 1099-r's one for the RMD, one for the ROTH funding as a normal distribution. Run the RMD one as the Indirect rollover the other as a Normal Distribution see how that flows onto the 1040. You really haven't altered anything, as all funds from the original 1099-R are accounted for .. they just get split. Think of it as taking your RMD with custodian A and doing your Roth conversion with custodian B... you would get 2 1099-R's...correct? Crank up TT load your return, then do a SAVE AS with a new name and use that return to experiment.
But I'd still probably give TT a call and tell the CSR to pass you through to one of their higher level support folks. If you know a CPA (who might be familiar with TT...) try that....
