I am sorry to hear you are running into issues with your valves not shutting correctly, and for the wasted time! This issue does sound a lot like a valve getting stuck open, however if the issue arose right when you installed your Gen 1 controller that does seem suspicious. Thank you for the wiring photos, those are very helpful.
There are a couple one time tests that would be really helpful for me to troubleshoot:
Could you run a "trouble" zone manually from the app, and push the faceplate firmly against the wall mount when the valve should be opening and when it should be closing (right at the beginning and the end of the run?) The faceplate is receiving the power for the rest of the system, and if the connection between that and the wall mount is weak, there is a chance there is not enough current to close the valve.
If that doesn't help the leaking, can you move both your common wires to one of the common terminals and manually run the zone? There is a chance one of the common terminals could be faulty, which would also reduce the current to your solenoids.
Let me know how these go and if any of those steps resolve the issue, and we can move forward from there! We never like to hear that we have an unhappy customer, we will make sure to get you back up and running