Are you able to share the Route Layer you created with me temporarily? I can take a look at what's going on, but be aware that current released Navigator is going to only use the stops provided in the Route Layer and re-calculate the route on the device. Therefore, any additional settings (time at stops, barriers, etc.) will not be honored. The next version of Navigator will honor these settings and use the exact route generated from the VRP tool.
Feel free to shoot me an email at jwhitney@esri.com and we can discuss further!
