My thought is that you didn't have enough pressure/volume for the valves to close properly. Valves react much differently under air pressure than they do with water pressure.
Close a shutoff valve to allow the tank to recharge. While it is recharging, check that all bleed screws, selonoids, etc. are tight and not manually running the zones. Also, tap on the top of the valve and selonoid with the but of a screwdriver. This is in an attempt to get a stuck diaphragm to reseat itself.
Start with zone 1. Once it is cleared, go to zone 2 and so forth allowing you tank to recharge as needed. It's not an uncommon problem. There are some valve brands that will not open once water has been eliminated from the mainline. Others won't open a second time. Some, like yours, won't shut off.
If able, it is best to keep the water moving in one direction towards the end/s of the mainline, clearing each valve in order as it goes. This process ensures that water will open every valve vs. a valve that is opened by air. Not always doable, I know, but it's what I strive for.