It still sounds like a bad diaphragm. They can get stiff and not open all the way via the timer but will open all the way when you open the bleed screw. As far as not shutting off goes. Here's three reasons off the top of my head. One, the diaphragm is stiff and doesn't want to close after you opened it all the way. Two, the old diaghpragm has a hole in it. Three, the flow control is open too far or you don't have a flow control at all. There's more but you can see there's something wrong with the valve. You either need a new diaphragm which should fix the problem or replace the whole valve. I'd still be asking myself where the water in the box is coming from. Your expert should have repaired the valve. He knew it wasn't fixed. Good luck!
If I can't fix it, it's broken!