I am having the same problem with my new Rachio 3 setup. Support told me it is likely trouble with the indexing valve. It’s unlikely that my indexing valve is experiencing a problem at the exact time I install the Rachio 3. The app shows that watering is advancing from one zone to the next; however only the first zone continues to run and will not shut off until the entire 4-zone watering cycle is complete (or if I stop it manually). Wondering if you’ve been able to resolve your issue.