"No changes to routing for fares that are flight specific or require specific routing."
Your broken fare was likely constructed from the separate SLC-JFK and JFK-BOS segments which would be "flight specific" tickets. I'm guessing this was cheaper than the SLC-BOS non-stop. By a strict reading of the SDC rules, the agent was correct. As noticed, the computers (and sometimes the agents) don't always follow the rules.