Valve acting up
I don't know your symptoms but it appears you've checked everything so I'll run with the diaphragm. Sometimes a diaphragm will appear to be ok but the rubber is a tad stiff. It's not as flexible as it used to be. This can cause a valve to be slow to come on or slow to turn off. Possibly stick on or not come on at all. Or come on part way. If you'd just changed the diaphragm instead of the whole bonnet you might have fixed the problem.
If I can't fix it, it's broken!