Look to see if you used the cycle and soak option. The system may be not watering for the total scheduled run time, it could be allowing the water to soak in. Select the watering icon (green or blue water drop) to review the details of the scheduled run for any date.
You might want to initially set up most of your zones on a fixed schedule using the same run times as from your old controller, and try a flex schedule for one or two zones as a start. Once you are happy with how the Rachio works, you can add more zones to the flex schedule, and tune them as needed.