I've had the same problems with my water pump on my 2GM and three different engineers have thought that the hoses had delaminated, the anti syphon valve had failed or the thermostat had seized. All things that I'd checked anyhow.
It runs from cold for as long as I want pumping water from the back but as soon as I shut it down, sail for a bit and then start it up the pump fails.
My thinking was this - the cam and inside face of the pump have worn enough from sand/silt that a warm engine creates a pressure differential in the cooling system to prevent a failing/failed pump to pump - but running from cold the cooling system, once pumping, will syphon.
However, the notion of the pulley spinning on the spindle (above) also works in my mind, i.e. the pump works and syphons from cold but a hot (and expanded) pulley will not pump although visually all looks good.
I'll check the pulley at the weekend but regardless I'm buying a new pump.
But, here's the thing. A replacement raw pump - about 40 litres a minute costs £366 but a freshwater pump (exactly the same mounts but a bigger impeller) costs £120 and pumps around 50 litres a minute.
I'm sure that the thermostat will regulate the flow through the engine anyway, but has anybody got any experience of increasing the flow in this way? I spoke to Yanmar UK and they told me to fit the raw water pump but had no advice regarding the freshwater pump.