I believe TT showing your 1099R assets as income is in error. The same thing happened to me but I kept on going and when I completed the section titled IRA calculation tool the 1099R asset had been removed.
What you want to watch is line 15a on form 1040. 15a must have the asset amount from box1 and the word ROLLOVER. Continue with the TT interview questions and I believe it will give what you want.