The plastic ball valve close to the ground isn't quite shut off. In any event, Your sprinkler system does not have an acceptable backflow preventer, so you want to take care of that as part of the repair process.
A one-size-fits-all solution starts with removing what you call the "Lawn Genie" and replacing it with a Pressure Vacuum Breaker, which is the actual code-approved device that should have been there in the first place. A secondary addition that will provide effective insurance from leaks further down the line is anther electric valve, like the ones you show in a valve box, that will feed the entire system. That electric valve is known as a "master valve", and it receives its power from the terminal on your controller marked MV ~ and don't use the cheapest possible master valve you find at the home center (although a Lawn Genie brand valve will be sufficient)
You have other issues in that system. water flowing from a sprinkler head 24/7 indicates the valve feeding it is not completely shutting off.