Bottom line, I didn’t have a master valve; however, the Hunter 12-zone, I replaced with the Rachio 16-zone, Gen-3 made me believe that I did have one (master valve). If you plug a wire into the “Master Valve” insert, (doesn’t matter which wire you incorrectly select as the Master Valve wire) whatever zone you select afterward (Z-2, Z-3, Z-5, etc.) will water every zone at the same time. Very frustrating!
Thankfully, I read here by another member of the Rachio community; they had done the same thing. So, if this happens to you, look for a misidentified “Master Valve” wire (black insert). It is actually a “Zone-X” and not a “Master Valve.” Unplug it from the black “Master Valve” insert, and plug it into any empty Zone insert.
Select it and check to see if that new zone is now watering. If it is, problem solved. You just incorrectly assumed the large black wire belonged in the black “Master Valve” insert, as I did.