In the 1099-R interview, after you entered the actual 1099-R data, how did you answer the question, "What did you do with the money from [name of plan]?" Did you answer "[name] moved the money to another retirement account (or returned it to the same retirement account)"/
If so, you would have seen an additional question that asked, "[name] rolled over all of this money to an IRA or other retirement account". When you check this line, then the 1099-R distribution would be considered nontaxable.